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- EMDB-55368: Noc2-TAP pre-60S particle - state 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-55368
TitleNoc2-TAP pre-60S particle - state 2
Map data
Sample
  • Complex: Noc2-TAP pre-60S particle - state 2
KeywordspreLSU / preribosome / complex / Noc2-TAP particle / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGrundmann L / Gerhalter M / Prattes M / Grishkovskaya I / Kotisch H / Haselbach D / Bergler H
Funding support Austria, 1 items
OrganizationGrant numberCountry
Austrian Science FundPAT1908524 Austria
CitationJournal: Nucleic Acids Res / Year: 2026
Title: A comprehensive view on r-protein binding and rRNA domain structuring during early eukaryotic ribosome formation.
Authors: Magdalena Gerhalter / Michael Prattes / Lorenz Emanuel Grundmann / Irina Grishkovskaya / Enrico F Semeraro / Gertrude Zisser / Harald Kotisch / Juliane Merl-Pham / Stefanie M Hauck / David ...Authors: Magdalena Gerhalter / Michael Prattes / Lorenz Emanuel Grundmann / Irina Grishkovskaya / Enrico F Semeraro / Gertrude Zisser / Harald Kotisch / Juliane Merl-Pham / Stefanie M Hauck / David Haselbach / Helmut Bergler /
Abstract: Formation of the eukaryotic ribosomal subunits follows a strict regime to assemble ribosomal proteins (r-protein) with ribosomal RNAs (rRNA) while removing internal (ITS) and external (ETS) ...Formation of the eukaryotic ribosomal subunits follows a strict regime to assemble ribosomal proteins (r-protein) with ribosomal RNAs (rRNA) while removing internal (ITS) and external (ETS) transcribed rRNA spacers. During the early stages of large subunit (LSU) formation, ITS2, together with six assembly factors, forms the characteristic foot structure of early nuclear pre-LSU particles. Here, we address the function of this foot structure during the early stages of ribosome assembly. We present cryo-EM structures from wild-type cells and cells depleted for the foot structure factor Rlp7. We show that compaction of domain I of the 25S rRNA is strictly dependent on the presence of foot factors, while domain II folds independently. Furthermore, Rlp7-depletion accumulated small subunit (SSU) processome intermediates prior to A1 cleavage and compaction of the individual domains of the 18S rRNA, providing also novel insights into the SSU-assembly process. SILAC labeling and affinity purification of co-transcriptionally assembled pre-ribosomes enabled us to resolve the assembly line of most early binding r-proteins step by step. This showed that incorporation of r-proteins in eukaryotes neither follows the bacterial regime nor a strict linear co-transcriptional mode. Instead, seed r-proteins might structurally define the individual rRNA domains before their compaction and fixation in the context of early pre-ribosomes.
History
DepositionOct 14, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55368.png

Downloads & links

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Map

FileDownload / File: emd_55368.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 400 pix.
= 536. Å		1.34 Å/pix.
x 400 pix.
= 536. Å		1.34 Å/pix.
x 400 pix.
= 536. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.281
Minimum - Maximum-0.7886247 - 1.8724227
Average (Standard dev.)0.00040179683 (±0.055326335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 536.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55368_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_55368_half_map_2.map
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Sample components

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Entire : Noc2-TAP pre-60S particle - state 2

EntireName: Noc2-TAP pre-60S particle - state 2
Components
  • Complex: Noc2-TAP pre-60S particle - state 2

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Supramolecule #1: Noc2-TAP pre-60S particle - state 2

SupramoleculeName: Noc2-TAP pre-60S particle - state 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16 / Details: Noc2-TAP particle from untreated yeast
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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
GridModel: Quantifoil R3.5/1 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11250 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.0 - 4.6) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0 - 4.6) / Number images used: 16006
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.0 - 4.6)
FSC plot (resolution estimation)

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