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- EMDB-29918: 80S Giardia lamblia ribosome at 2.67 angstroms resolution with Em... -

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Basic information

Entry
Database: EMDB / ID: EMD-29918
Title80S Giardia lamblia ribosome at 2.67 angstroms resolution with Emetine in the the V2 conformation
Map data
Sample
  • Complex: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome
KeywordsGiardia lamblia / Ribosome structure / Translation / parasite / RIBOSOME
Biological speciesGiardia intestinalis assemblage A (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsEiler DR / Wimberly BT / Bilodeau DY / Rissland OS / Kieft JS
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118070 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI149210 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128680 United States
CitationJournal: Structure / Year: 2024
Title: The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function.
Authors: Daniel R Eiler / Brian T Wimberly / Danielle Y Bilodeau / J Matthew Taliaferro / Philip Reigan / Olivia S Rissland / Jeffrey S Kieft /
Abstract: Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure ...Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure of the G. lamblia 80S ribosome bound to tRNA, mRNA, and the antibiotic emetine by cryo-electron microscopy, to an overall resolution of 2.49 Å. The structure reveals rapidly evolving protein and nucleotide regions, differences in the peptide exit tunnel, and likely altered ribosome quality control pathways. Examination of translation initiation factor binding sites suggests these interactions are conserved despite a divergent initiation mechanism. Highlighting the potential of G. lamblia to resolve conserved biological principles; our structure reveals the interactions of the translation inhibitor emetine with the ribosome and mRNA, thus providing insight into the mechanism of action for this widely used antibiotic. Our work defines key questions in G. lamblia and motivates future experiments to explore the diversity of eukaryotic gene regulation.
History
DepositionFeb 26, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29918.png

Downloads & links

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Map

FileDownload / File: emd_29918.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8211 Å
Density
Contour LevelBy AUTHOR: 0.447
Minimum - Maximum-1.2391211 - 3.2945526
Average (Standard dev.)-0.003470369 (±0.07425174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions702702702
Spacing702702702
CellA=B=C: 576.4122 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29918_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29918_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 60S ribosomal subunit of the 80S Giardia intestinalis assemblage ...

EntireName: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome
Components
  • Complex: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome

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Supramolecule #1: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage ...

SupramoleculeName: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Giardia intestinalis assemblage A (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 72.26 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xy3

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146223
FSC plot (resolution estimation)

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