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- EMDB-16038: hexameric ct-sc 5S RNP dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-16038
Titlehexameric ct-sc 5S RNP dimer
Map dataHexameric ct-sc 5S RNP dimer (Local filtered map, C2 symmetry) (containing Rpf2, Rrs1 and Syo1 from C. thermophilum and uL18/L5, uL5/L11 and 5S rRNA from S. cerevisiae)
Sample
  • Complex: hexameric ct-sc 5S RNP dimer
Keywords5S RNP / Ribosome biogenesis / Symportin 1 / Rpf2-Rrs1 / RNA BINDING PROTEIN
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsCastillo N / Thoms M / Flemming D / Hammaren HM / Buschauer R / Ameismeier M / Bassler J / Beck M / Beckmann R / Hurt E
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)RK1721 Germany
German Research Foundation (DFG)HU363/15-2 Germany
European Research Council (ERC)885711European Union
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2-p53 pathways.
Authors: Nestor Miguel Castillo Duque de Estrada / Matthias Thoms / Dirk Flemming / Henrik M Hammaren / Robert Buschauer / Michael Ameismeier / Jochen Baßler / Martin Beck / Roland Beckmann / Ed Hurt /
Abstract: The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is ...The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is disturbed, a free 5S RNP can enter the MDM2-p53 pathway to regulate cell cycle and apoptotic signaling. Here we reconstitute and determine the cryo-electron microscopy structure of the conserved hexameric 5S RNP with fungal or human factors. This reveals how the nascent 5S rRNA associates with the initial nuclear import complex Syo1-uL18-uL5 and, upon further recruitment of the nucleolar factors Rpf2 and Rrs1, develops into the 5S RNP precursor that can assemble into the pre-ribosome. In addition, we elucidate the structure of another 5S RNP intermediate, carrying the human ubiquitin ligase Mdm2, which unravels how this enzyme can be sequestered from its target substrate p53. Our data provide molecular insight into how the 5S RNP can mediate between ribosome biogenesis and cell proliferation.
History
DepositionOct 28, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16038.png

Downloads & links

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Map

FileDownload / File: emd_16038.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHexameric ct-sc 5S RNP dimer (Local filtered map, C2 symmetry) (containing Rpf2, Rrs1 and Syo1 from C. thermophilum and uL18/L5, uL5/L11 and 5S rRNA from S. cerevisiae)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 317.7 Å		1.06 Å/pix.
x 300 pix.
= 317.7 Å		1.06 Å/pix.
x 300 pix.
= 317.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-0.6369926 - 2.3106651
Average (Standard dev.)0.011067844 (±0.06795811)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Hexameric ct-sc 5S RNP dimer (Non-uniform Refinement, C2 symmetry)

Fileemd_16038_additional_1.map
AnnotationHexameric ct-sc 5S RNP dimer (Non-uniform Refinement, C2 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Hexameric ct-sc 5S RNP dimer (Non-uniform Refinement, C2...

Fileemd_16038_additional_2.map
AnnotationHexameric ct-sc 5S RNP dimer (Non-uniform Refinement, C2 symmetry, sharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Hexameric ct-sc 5S RNP dimer (half map A...

Fileemd_16038_half_map_1.map
AnnotationHexameric ct-sc 5S RNP dimer (half map A from the non-uniform Refinement, C2 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Hexameric ct-sc 5S RNP dimer (half map B...

Fileemd_16038_half_map_2.map
AnnotationHexameric ct-sc 5S RNP dimer (half map B from the non-uniform Refinement, C2 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hexameric ct-sc 5S RNP dimer

EntireName: hexameric ct-sc 5S RNP dimer
Components
  • Complex: hexameric ct-sc 5S RNP dimer

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Supramolecule #1: hexameric ct-sc 5S RNP dimer

SupramoleculeName: hexameric ct-sc 5S RNP dimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68563
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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