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- PDB-6yle: Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body ... -

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Database: PDB / ID: 6yle
TitleRix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement)
  • Pre-rRNA-processing protein IPI1
  • Pre-rRNA-processing protein IPI3
  • Pre-rRNA-processing protein RIX1
KeywordsRIBOSOME / pre-60S / Biogenesis / LSU / Large subunit / ribosome assembly
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)
MethodELECTRON MICROSCOPY / single 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 Report
SummaryFull reportAbout validation report
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release

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Deposited unit
A: Pre-rRNA-processing protein IPI3
B: Pre-rRNA-processing protein IPI3
C: Pre-rRNA-processing protein RIX1
D: Pre-rRNA-processing protein RIX1
K: Pre-rRNA-processing protein IPI1

Theoretical massNumber of molelcules
Total (without water)335,2825

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26700 Å2
ΔGint-157 kcal/mol
Surface area74500 Å2


#1: Protein Pre-rRNA-processing protein IPI3 / Involved in processing IST2 protein 3

Mass: 61836.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53877
#2: Protein Pre-rRNA-processing protein RIX1 / Involved in processing IST2 protein 2 / Ribosomal export protein 1

Mass: 86839.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38883
#3: Protein Pre-rRNA-processing protein IPI1 / Involved in processing IST2 protein 1

Mass: 37928.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZSZ4

Experimental details


EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Rix1-Rea1 pre-60S assembly particle - Rix1-subcomplex / Type: RIBOSOME
Details: Rix1-TAP Flag-Rea1 derived pre-60S assembly complex
Entity ID: 1, 2, 3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 10 sec. / Electron dose: 75 e/Å2 / Detector mode: INTEGRATING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 48 / Used frames/image: 1-48


EM software
1RELION3.0.8particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELION3.0.8initial Euler assignment
11RELION3.0.8final Euler assignment
13RELION3.0.83D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 273799
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114398 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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