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- EMDB-10836: Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10836
TitleRix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement)
Map data
SampleRix1-Rea1 pre-60S assembly particle - Rix1-subcomplex:
(Pre-rRNA-processing protein ...) x 3
Function / homology
Function and homology information


Rix1 complex / regulation of DNA-dependent DNA replication initiation / nuclear pre-replicative complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / rRNA processing / ribosomal large subunit assembly / chromatin binding / nucleoplasm / nucleus / cytosol
WD40 repeat / Armadillo-type fold / Testis-expressed protein 10/pre-rRNA-processing protein Ipi1 / WD40-repeat-containing domain superfamily / Pre-rRNA-processing protein Ipi1, N-terminal / WD40-repeat-containing domain / Pre-rRNA-processing protein RIX1, N-terminal / WD40/YVTN repeat-like-containing domain superfamily
Pre-rRNA-processing protein IPI1 / Pre-rRNA-processing protein RIX1 / Pre-rRNA-processing protein IPI3
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKater L / Beckmann R
CitationJournal: Mol. Cell / Year: 2020
Title: Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Authors: Lukas Kater / Valentin Mitterer / Matthias Thoms / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering ...Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix1-Ipi3 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.
Validation ReportPDB-ID: 6yle

SummaryFull reportAbout validation report
History
DepositionApr 7, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yle
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yle
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10836.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 211.8 Å
1.06 Å/pix.
x 200 pix.
= 211.8 Å
1.06 Å/pix.
x 200 pix.
= 211.8 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
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.037551817 - 0.072617956
Average (Standard dev.)0.00043897267 (±0.0037487403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z211.800211.800211.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0380.0730.000

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Supplemental data

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Half map: Relion half map (unfiltered, unmasked)

Fileemd_10836_half_map_1.map
AnnotationRelion half map (unfiltered, unmasked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Relion half map (unfiltered, unmasked)

Fileemd_10836_half_map_2.map
AnnotationRelion half map (unfiltered, unmasked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex

EntireName: Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex
Details: Rix1-TAP Flag-Rea1 derived pre-60S assembly complex
Number of components: 4

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Component #1: protein, Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex

ProteinName: Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex
Details: Rix1-TAP Flag-Rea1 derived pre-60S assembly complex
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, Pre-rRNA-processing protein IPI3

ProteinName: Pre-rRNA-processing protein IPI3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 61.836695 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #3: protein, Pre-rRNA-processing protein RIX1

ProteinName: Pre-rRNA-processing protein RIX1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 86.839844 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #4: protein, Pre-rRNA-processing protein IPI1

ProteinName: Pre-rRNA-processing protein IPI1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.928895 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 75 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 5 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 114398
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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