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- EMDB-55840: Noc2-TAP pre-60S particle - state 3 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-55840
TitleNoc2-TAP pre-60S particle - state 3
Map data
Sample
  • Complex: Yeast pre-60S Domain II
KeywordspreLSU / preribosome / complex / Noc2-TAP particle / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGerhalter M / Prattes M / Grundmann L / Grishkovskaya I / Kotisch H / Haselbach D / Bergler H
Funding support Austria, 1 items
OrganizationGrant numberCountry
Austrian Science FundPAT1908524 Austria
CitationJournal: To Be Published
Title: A comprehensive view on r- protein binding and rRNA domain structuring during early ribosome formation
Authors: Gerhalter M / Prattes M / Grundmann L / Grishkovskaya I / Semarari EF / Zisser G / Harald K / Merl-Pharm J / Hauck SM / Haselbach D / Bergler H
History
DepositionNov 26, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55840.png

Downloads & links

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Map

FileDownload / File: emd_55840.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.302
Minimum - Maximum-0.7664798 - 2.002761
Average (Standard dev.)0.0006574302 (±0.060435046)
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_55840_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_55840_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 : Yeast pre-60S Domain II

EntireName: Yeast pre-60S Domain II
Components
  • Complex: Yeast pre-60S Domain II

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Supramolecule #1: Yeast pre-60S Domain II

SupramoleculeName: Yeast pre-60S Domain II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Details: Noc2-TAP particle from yeast after Rpl7 depletion, where only Domain II adopts a structured conformation
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: 15424
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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