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- EMDB-29111: Human nucleolar pre-60S ribosomal subunit (State D2) - Overall map -

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Basic information

Entry
Database: EMDB / ID: EMD-29111
TitleHuman nucleolar pre-60S ribosomal subunit (State D2) - Overall map
Map dataLocal resolution filtered map
Sample
  • Complex: Human nucleolar pre-60S ribosomal subunit (State D2)
KeywordsPre-60S ribosomal subunit / Assembly intermediate / Ribosome / Nucleoprotein complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsVanden Broeck A / Klinge S
Funding supportEuropean Union, United States, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 711-2019European Union
The G. Harold and Leila Y. Mathers FoundationMF-2104-01554 United States
CitationJournal: Science / Year: 2023
Title: Principles of human pre-60 biogenesis.
Authors: Arnaud Vanden Broeck / Sebastian Klinge /
Abstract: During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an ...During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60 particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation.
History
DepositionDec 15, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29111.png

Downloads & links

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Map

FileDownload / File: emd_29111.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 480 pix.
= 514.56 Å		1.07 Å/pix.
x 480 pix.
= 514.56 Å		1.07 Å/pix.
x 480 pix.
= 514.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-2.5499558 - 4.6054783
Average (Standard dev.)0.008213236 (±0.07104544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 514.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29111_msk_1.map
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AxesZYX

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Additional map: Phenix auto-sharpened map

Fileemd_29111_additional_1.map
AnnotationPhenix auto-sharpened map
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Additional map: cryoSPARC sharpened map

Fileemd_29111_additional_2.map
AnnotationcryoSPARC sharpened map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_29111_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29111_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human nucleolar pre-60S ribosomal subunit (State D2)

EntireName: Human nucleolar pre-60S ribosomal subunit (State D2)
Components
  • Complex: Human nucleolar pre-60S ribosomal subunit (State D2)

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Supramolecule #1: Human nucleolar pre-60S ribosomal subunit (State D2)

SupramoleculeName: Human nucleolar pre-60S ribosomal subunit (State D2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#47
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293F

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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: 7.6
GridModel: Quantifoil R3.5/1 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
Details: Four applications with manual blotting before last blotting with the vitrobot..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 172699 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 15679142
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 214795
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationSoftware: (Name: RELION (ver. 4.0), cryoSPARC (ver. 3.3.2))
FSC plot (resolution estimation)

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