[English] 日本語
Yorodumi
- PDB-9v26: Cryo- EM structure of 75S ribosome with A/P- & P/E- tRNAs from En... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9v26
TitleCryo- EM structure of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica bound to antibiotic paromomycin
Components
  • (40S ribosomal protein ...) x 18
  • (60S ribosomal protein ...) x 30
  • (Large ribosomal subunit protein ...) x 4
  • (Ribosomal protein ...) x 7
  • (Small ribosomal subunit protein ...) x 7
  • 17S rRNA
  • 25S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • A/P-tRNA
  • P/E-tRNA
  • mRNA
  • uL29
KeywordsRIBOSOME / 75S Ribosome-PAR complex / A/P-tRNA / P/E-tRNA / Entamoeba histolytica
Function / homology
Function and homology information


inositol hexakisphosphate binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / maturation of LSU-rRNA / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA ...inositol hexakisphosphate binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / maturation of LSU-rRNA / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / endoplasmic reticulum / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
PUA domain profile. / Ribosomal protein L30e / : / Ribosomal protein L2, archaeal-type / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site ...PUA domain profile. / Ribosomal protein L30e / : / Ribosomal protein L2, archaeal-type / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L10e / Ribosomal protein L44e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / : / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / 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. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal Protein L6, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / : / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / 60S ribosomal protein L19 / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S19A/S15e / Ribosomal protein L13, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S17e / Ribosomal protein L7A/L8 / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 60S ribosomal protein L6E / Ribosomal protein L30/YlxQ / Ribosomal protein L18e / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L36e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e
Similarity search - Domain/homology
PAROMOMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S13, putative / 60S ribosomal protein L38 putative ...PAROMOMYCIN / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S13, putative / 60S ribosomal protein L38 putative / 60S ribosomal protein L37a, putative / Ribosomal protein S14, putative / Large ribosomal subunit protein uL4 / 60S ribosomal protein L35a, putative / 60S ribosomal protein L44, putative / 60S ribosomal protein L24, putative / 60S ribosomal protein L26, putative / 40S ribosomal protein S3 / 60S ribosomal protein L32, putative / Ribosomal protein L10, putative / Ribosomal protein L39, putative / 60S ribosomal protein L31, putative / 60S ribosomal protein L5, putative / 60S ribosomal protein L29 / 60S ribosomal protein L40, putative / Ribosomal protein L23A, putative / 60S ribosomal protein L21, putative / 60S ribosomal protein L23, putative / 40S ribosomal protein S10, putative / 60S ribosomal protein L7a / 60S ribosomal protein L9, putative / 60S ribosomal protein L3, putative / Ribosomal protein S29, putative / Large ribosomal subunit protein eL22 / Ribosomal protein L19 / 40S ribosomal protein S21 / 60S ribosomal protein L17, putative / 60S ribosomal protein L18, putative / 40S ribosomal protein S15a, putative / 40S ribosomal protein S6 / 60S ribosomal protein L18a / 60S ribosomal protein L34, putative / 40S ribosomal protein S4, putative / 60S ribosomal protein L11, putative / 60S ribosomal protein L36, putative / 40S ribosomal protein S28, putative / 60S ribosomal protein L37-A, putative / 40S ribosomal protein S17, putative / 40S ribosomal protein S16, putative / 60S ribosomal protein L13, putative / 40S ribosomal protein S23, putative / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / 60S ribosomal protein L27, putative / 60S ribosomal protein L7, putative / 40S ribosomal protein S26 / 40S ribosomal protein S15, putative / Small ribosomal subunit protein uS5 / Ribosomal protein L15 / 60S ribosomal protein L14, putative / 60S ribosomal protein L13, putative / 40S ribosomal protein S8 / 60S ribosomal protein L30, putative / 40S ribosomal protein S11, putative / 40S ribosomal protein S25 / 40S ribosomal protein S7 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL6 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL15A
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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
lA: 25S rRNA
lB: 5.8S rRNA
lC: 5S rRNA
lD: Large ribosomal subunit protein uL2
lE: 60S ribosomal protein L3, putative
lF: 60S ribosomal protein L4, putative
lG: 60S ribosomal protein L5, putative
lH: Large ribosomal subunit protein eL6
lI: 60S ribosomal protein L7, putative
lJ: 60S ribosomal protein L7a
lK: 60S ribosomal protein L9, putative
lL: Ribosomal protein L10, putative
lM: 60S ribosomal protein L11, putative
lN: 60S ribosomal protein L13, putative
lO: 60S ribosomal protein L13, putative
lP: 60S ribosomal protein L14, putative
lQ: Ribosomal protein L15
lR: 60S ribosomal protein L17, putative
lS: 60S ribosomal protein L18, putative
lT: 60S ribosomal protein L18a
lU: Ribosomal protein L19
lV: 60S ribosomal protein L21, putative
lW: Large ribosomal subunit protein eL22
lX: 60S ribosomal protein L23, putative
lY: Ribosomal protein L23A, putative
lZ: 60S ribosomal protein L24, putative
la: 60S ribosomal protein L26, putative
lb: 60S ribosomal protein L27, putative
lc: Large ribosomal subunit protein uL15A
ld: 60S ribosomal protein L29
le: 60S ribosomal protein L30, putative
lf: 60S ribosomal protein L31, putative
lg: 60S ribosomal protein L32, putative
lh: 60S ribosomal protein L34, putative
li: uL29
lj: 60S ribosomal protein L35a, putative
lk: 60S ribosomal protein L36, putative
ll: 60S ribosomal protein L37-A, putative
lm: 60S ribosomal protein L37a, putative
ln: 60S ribosomal protein L38 putative
lo: Ribosomal protein L39, putative
lp: 60S ribosomal protein L40, putative
lq: 60S ribosomal protein L44, putative
sA: 40S ribosomal protein S25
sB: 40S ribosomal protein S26
sC: Small ribosomal subunit protein eS27
sD: 40S ribosomal protein S28, putative
sE: Ribosomal protein S29, putative
sI: A/P-tRNA
sJ: P/E-tRNA
sK: mRNA
sa: 17S rRNA
sc: Small ribosomal subunit protein uS5
sd: 40S ribosomal protein S3
se: Small ribosomal subunit protein eS1
sf: 40S ribosomal protein S4, putative
sg: Small ribosomal subunit protein uS7
sh: 40S ribosomal protein S6
si: 40S ribosomal protein S7
sj: 40S ribosomal protein S8
sk: Small ribosomal subunit protein uS4
sl: 40S ribosomal protein S10, putative
sm: 40S ribosomal protein S11, putative
so: 40S ribosomal protein S13, putative
sp: Ribosomal protein S14, putative
sq: 40S ribosomal protein S15, putative
sr: 40S ribosomal protein S15a, 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
sx: 40S ribosomal protein S21
sy: 40S ribosomal protein S23, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,174,41175
Polymers3,173,79674
Non-polymers6161
Water00
1


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

-
Components

-
RNA chain , 7 types, 7 molecules lAlBlCsIsJsKsa

#1: RNA chain 25S rRNA


Mass: 1130459.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: GenBank: BDEQ01000001
#2: RNA chain 5.8S rRNA


Mass: 49892.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: GenBank: 415339
#3: RNA chain 5S rRNA


Mass: 37450.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: GenBank: 61658858
#49: RNA chain A/P-tRNA


Mass: 24483.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
#50: RNA chain P/E-tRNA


Mass: 24632.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
#51: 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)
#52: 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

-
Large ribosomal subunit protein ... , 4 types, 4 molecules lDlHlWlc

#4: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L2 / 60S ribosomal protein L8


Mass: 27850.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: O15574
#8: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6


Mass: 22958.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: O15595
#23: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 15877.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LW40
#29: Protein Large ribosomal subunit protein uL15A / 60S ribosomal protein L27a-1


Mass: 17042.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: Q9BI06

+
60S ribosomal protein ... , 30 types, 30 molecules lElFlGlIlJlKlMlNlOlPlRlSlTlVlXlZlalbldlelflglhljlklllmlnlplq

#5: Protein 60S ribosomal protein L3, putative


Mass: 45620.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LW09
#6: Protein 60S ribosomal protein L4, putative


Mass: 47430.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: B1N384
#7: Protein 60S ribosomal protein L5, putative


Mass: 32437.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LU56
#9: Protein 60S ribosomal protein L7, putative


Mass: 25765.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M751
#10: Protein 60S ribosomal protein L7a


Mass: 32313.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LVH6
#11: Protein 60S ribosomal protein L9, putative


Mass: 22351.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LVZ9
#13: Protein 60S ribosomal protein L11, putative


Mass: 19669.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LZG9
#14: Protein 60S ribosomal protein L13, putative


Mass: 33028.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M8R8
#15: Protein 60S ribosomal protein L13, putative


Mass: 23177.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M3F3
#16: Protein 60S ribosomal protein L14, putative


Mass: 15161.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M8C9
#18: Protein 60S ribosomal protein L17, putative


Mass: 19892.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LX05
#19: Protein 60S ribosomal protein L18, putative


Mass: 19038.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LXC8
#20: Protein 60S ribosomal protein L18a


Mass: 20130.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LXZ0
#22: Protein 60S ribosomal protein L21, putative


Mass: 18869.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LV69
#24: Protein 60S ribosomal protein L23, putative


Mass: 15260.810 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LVB0
#26: Protein 60S ribosomal protein L24, putative


Mass: 18649.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LSA0
#27: Protein 60S ribosomal protein L26, putative


Mass: 23898.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LSU3
#28: Protein 60S ribosomal protein L27, putative


Mass: 15786.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M727
#30: Protein 60S ribosomal protein L29


Mass: 7340.583 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LUN3
#31: Protein 60S ribosomal protein L30, putative


Mass: 11629.423 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M919
#32: Protein 60S ribosomal protein L31, putative


Mass: 17281.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LU13
#33: Protein 60S ribosomal protein L32, putative


Mass: 15572.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LT96
#34: Protein 60S ribosomal protein L34, putative


Mass: 15481.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LYA7
#36: Protein 60S ribosomal protein L35a, putative


Mass: 12143.319 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: B1N4V3
#37: Protein 60S ribosomal protein L36, putative


Mass: 11942.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LZH1
#38: Protein 60S ribosomal protein L37-A, putative


Mass: 9046.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M0X0
#39: Protein 60S ribosomal protein L37a, putative


Mass: 10321.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: A0A175JXH6
#40: Protein 60S ribosomal protein L38 putative


Mass: 8795.554 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: A0A175JTS8
#42: Protein 60S ribosomal protein L40, putative


Mass: 6482.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LV09
#43: Protein 60S ribosomal protein L44, putative


Mass: 11603.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LS99

-
Ribosomal protein ... , 7 types, 7 molecules lLlQlUlYlosEsp

#12: Protein Ribosomal protein L10, putative


Mass: 23831.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LTA0
#17: Protein Ribosomal protein L15


Mass: 23951.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M7U2
#21: Protein Ribosomal protein L19


Mass: 22978.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LWJ4
#25: Protein Ribosomal protein L23A, putative


Mass: 13694.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LV64
#41: Protein Ribosomal protein L39, putative


Mass: 6282.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LTA2
#48: 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
#65: 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

-
40S ribosomal protein ... , 18 types, 18 molecules sAsBsDsdsfshsisjslsmsosqsrssstswsxsy

#44: 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
#45: 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
#47: 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
#54: 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
#56: 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
#58: 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
#59: 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
#60: Protein 40S ribosomal protein S8


Mass: 27017.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M8Y8
#62: 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
#63: 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
#64: 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
#66: 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
#67: 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
#68: 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
#69: 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
#72: 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
#73: Protein 40S ribosomal protein S21


Mass: 9582.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LWW3
#74: 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

-
Small ribosomal subunit protein ... , 7 types, 7 molecules sCscsesgsksusv

#46: 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
#53: 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
#55: 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
#57: 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
#61: 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
#70: 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
#71: 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 / Non-polymers , 2 types, 2 molecules li

#35: Protein uL29


Mass: 13925.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
#75: 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

-
Details

Has ligand of interestY
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 75S ribosome bound to Paromomycin with A/P and P/E-tRNA from Entamoeba histolytica
Type: RIBOSOME / Entity ID: #1-#74 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote) / Cellular location: cytoplasm / 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: 1.09 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 4688

-
Processing

EM software
IDNameVersionCategory
1RELION3.1.4particle selection
2PHENIXdev_svnmodel refinement
5CTFFINDCTF correction
10RELION3.1.4initial Euler assignment
11RELION3.1.4final Euler assignment
12RELION3.1.4classification
13RELION3.1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 85291
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54889 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 29.97 / 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