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- EMDB-29897: Focused refinement of the 40S subunit head of the 80S Giardia lam... -

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Basic information

Entry
Database: EMDB / ID: EMD-29897
TitleFocused refinement of the 40S subunit head of the 80S Giardia lamblia ribosome at 2.94 angstroms resolution.
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: 2.94 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)R35GM118070 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI149210 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128680 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 22, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29897.png

Downloads & links

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Map

FileDownload / File: emd_29897.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 450 pix.
= 369.495 Å		0.82 Å/pix.
x 450 pix.
= 369.495 Å		0.82 Å/pix.
x 450 pix.
= 369.495 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8211 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.171
Minimum - Maximum-1.0292923 - 2.4640195
Average (Standard dev.)-0.010388785 (±0.05119039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 369.495 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29897_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29897_half_map_2.map
Projections & Slices
AxesZYX

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 72.26 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.5 µm
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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 289618
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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