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- PDB-9v1i: Cryo- EM structure of ribosomal large subunit (LSU) from Entamoeb... -

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Basic information

Entry
Database: PDB / ID: 9v1i
TitleCryo- EM structure of ribosomal large subunit (LSU) from Entamoeba histolytica at 2.8 angstrom resolution
Components
  • (60S ribosomal protein ...) x 31
  • (Large ribosomal subunit protein ...) x 3
  • (Ribosomal protein ...) x 5
  • 25S rRNA (3068-MER)
  • 5.8S rRNA (145-MER)
  • 5S rRNA (117-MER)
  • Unknown peptide
  • uL29
KeywordsRIBOSOME / LSU / Entamoeba histolytica / 53S
Function / homology
Function and homology information


protein-RNA complex assembly / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...protein-RNA complex assembly / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / endoplasmic reticulum / RNA binding / zinc ion binding
Similarity search - Function
Ribosomal protein L30e / : / Ribosomal protein L2, archaeal-type / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily ...Ribosomal protein L30e / : / Ribosomal protein L2, archaeal-type / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal L40e family / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / 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 / : / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L6e / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L6E / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L18e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L14e domain / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L14 / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L32e / Ribosomal protein L37ae/L37e
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4 / 60S ribosomal protein L35a, putative / 60S ribosomal protein L44, putative ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / 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 / 60S ribosomal protein L7a / 60S ribosomal protein L9, putative / 60S ribosomal protein L3, putative / Large ribosomal subunit protein eL22 / Ribosomal protein L19 / 60S ribosomal protein L17, putative / 60S ribosomal protein L18, putative / 60S ribosomal protein L18a / 60S ribosomal protein L34, putative / Large ribosomal subunit protein eL6 / 60S ribosomal protein L11, putative / 60S ribosomal protein L36, putative / 60S ribosomal protein L37-A, putative / 60S ribosomal protein L13, putative / 60S ribosomal protein L38, putative / 60S ribosomal protein L27, putative / 60S ribosomal protein L7, putative / Ribosomal protein L15 / 60S ribosomal protein L14, putative / 60S ribosomal protein L13, putative / 60S ribosomal protein L30, putative / 60S ribosomal protein L37A, putative / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL15A
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 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
lA: 25S rRNA (3068-MER)
lB: 5.8S rRNA (145-MER)
lC: 5S rRNA (117-MER)
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: 60S ribosomal protein L6, putative
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
lr: Unknown peptide


Theoretical massNumber of molelcules
Total (without water)1,994,14944
Polymers1,994,14944
Non-polymers00
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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RNA chain , 3 types, 3 molecules lAlBlC

#1: RNA chain 25S rRNA (3068-MER)


Mass: 1130459.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 25S rRNA
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: GenBank: BDEQ01000001
#2: RNA chain 5.8S rRNA (145-MER)


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 (117-MER)


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

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Large ribosomal subunit protein ... , 3 types, 3 molecules lDlWlc

#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
#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

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60S ribosomal protein ... , 31 types, 31 molecules lElFlGlHlIlJlKlMlNlOlPlRlSlTlVlXlZlalbldlelflglhljlklllmlnlplq

#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
#8: Protein 60S ribosomal protein L6, putative


Mass: 22944.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LYF9
#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: 10249.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: N9UZL4
#40: Protein 60S ribosomal protein L38, putative


Mass: 9586.526 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M6F9
#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

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Ribosomal protein ... , 5 types, 5 molecules lLlQlUlYlo

#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

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Protein / Protein/peptide , 2 types, 2 molecules lilr

#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)
#44: Protein/peptide Unknown peptide


Mass: 1124.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)

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Details

Has protein modificationY

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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: Entamoeba histolytica Ribosome Large Subunit / Type: RIBOSOME / Entity ID: all / 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

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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: 1.34 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 3470

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Processing

EM softwareName: PHENIX / Version: dev_svn / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 763731
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 378061 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 67.76 / Protocol: FLEXIBLE FIT / Space: REAL / Details: phenix.real_space_refinement
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15XXB

5xxb

15XXB1PDBexperimental model
24UG0

4ug0

14UG02PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 70.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036130731
ELECTRON MICROSCOPYf_angle_d0.5729192456
ELECTRON MICROSCOPYf_chiral_restr0.038724207
ELECTRON MICROSCOPYf_plane_restr0.004111889
ELECTRON MICROSCOPYf_dihedral_angle_d20.477553065

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  • 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

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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

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