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- EMDB-29906: 80S Giardia lamblia ribosome at 2.66 angstroms resolution with Em... -

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Basic information

Entry
Database: EMDB / ID: EMD-29906
Title80S Giardia lamblia ribosome at 2.66 angstroms resolution with Emetine in the the V1 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: 2.66 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: To Be Published
Title: The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function
Authors: Eiler DR / Wimberly BT / Bilodeau DY / Rissland OS / Kieft JS
History
DepositionFeb 23, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29906.png

Downloads & links

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Map

FileDownload / File: emd_29906.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 702 pix.
= 576.412 Å		0.82 Å/pix.
x 702 pix.
= 576.412 Å		0.82 Å/pix.
x 702 pix.
= 576.412 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8211 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.461
Minimum - Maximum-1.3818475 - 3.5210748
Average (Standard dev.)-0.0031938674 (±0.078856334)
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_29906_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_29906_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: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143395
FSC plot (resolution estimation)

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