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- EMDB-47217: Cryptococcus neoformans 40S Map -

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Basic information

Entry
Database: EMDB / ID: EMD-47217
TitleCryptococcus neoformans 40S Map
Map dataCryoptococcus neoformans 40S map
Sample
  • Complex: C. Neoformans 40S Ribosome
    • Other: C. Neoformans 40S Ribosome
Keywords40S ribosome / cryoEM / ribosome / cryptococcus / neoformans
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsErath J / Djuranovic S / Pavlovic Djuranovic S / Hashem Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136823 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112824 United States
CitationJournal: Nat Commun / Year: 2025
Title: A rapid, simple, and economical method for the isolation of ribosomes and translational machinery for structural and functional studies.
Authors: Jessey Erath / Danielle Kemper / Elisha Mugo / Alex Jacoby / Elizabeth Valenzuela / Courtney F Jungers / Wandy L Beatty / Yaser Hashem / Marko Jovanovic / Sergej Djuranovic / Slavica Pavlovic Djuranovic /
Abstract: Ribosomes are RNA-protein complexes essential for protein synthesis and quality control. Traditional methods for ribosome isolation are labor-intensive, expensive, and require a substantial amount of ...Ribosomes are RNA-protein complexes essential for protein synthesis and quality control. Traditional methods for ribosome isolation are labor-intensive, expensive, and require a substantial amount of biological material. In contrast, our method, RNA affinity purification using poly-lysine (RAPPL), provides a rapid, simple, and cost-effective alternative applicable to various species and types of starting material (cell lysates, whole cells, organs, or whole organisms). It is also compatible with traditional isolation techniques. Here, we describe the use of RAPPL for rapid isolation, functional screening, and structural analysis of ribosomes and associated factors. We also demonstrate the application of RAPPL in investigating ribosome-associated resistance mechanisms in uropathogenic Escherichia coli samples and generating a 2.7-Å cryoEM ribosome structure from Cryptococcus neoformans. By significantly reducing the amount of the starting biological material and the time required for isolation, RAPPL has the potential to facilitate the study of ribosomal function, interactions, and antibiotic resistance and provide a versatile platform for academic, clinical, and industrial research.
History
DepositionOct 8, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47217.png

Downloads & links

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Map

FileDownload / File: emd_47217.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoptococcus neoformans 40S map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 450 pix.
= 504.9 Å		1.12 Å/pix.
x 450 pix.
= 504.9 Å		1.12 Å/pix.
x 450 pix.
= 504.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-7.5288644 - 12.70356
Average (Standard dev.)-0.007682447 (±0.28596923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 504.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryoptococcus neoformans 40S map

Fileemd_47217_additional_1.map
AnnotationCryoptococcus neoformans 40S map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryoptococcus neoformans 40S half map

Fileemd_47217_half_map_1.map
AnnotationCryoptococcus neoformans 40S half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryoptococcus neoformans 40S half map

Fileemd_47217_half_map_2.map
AnnotationCryoptococcus neoformans 40S half 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 : C. Neoformans 40S Ribosome

EntireName: C. Neoformans 40S Ribosome
Components
  • Complex: C. Neoformans 40S Ribosome
    • Other: C. Neoformans 40S Ribosome

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Supramolecule #1: C. Neoformans 40S Ribosome

SupramoleculeName: C. Neoformans 40S Ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cryptococcus neoformans (Cryptococcus neoformans serotype A)

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Macromolecule #1: C. Neoformans 40S Ribosome

MacromoleculeName: C. Neoformans 40S Ribosome / type: other / ID: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
SequenceString:
none

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.6 µm / Nominal magnification: 59000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 294300
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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