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Open data
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Basic information
Entry | Database: PDB / ID: 6i27 | ||||||
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Title | Rea1 AAA2L-H2alpha deletion mutant in AMPPNP State | ||||||
![]() | Midasin,Midasin,Midasin,Midasin,Midasin,Midasin,Midasin | ||||||
![]() | MOTOR PROTEIN / Rea1 / Mdn1 / Midasin / AAA+ protein / ribosome maturation / molecular machine | ||||||
Function / homology | ![]() protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / ribosomal large subunit assembly / rRNA processing / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / ribosomal large subunit assembly / rRNA processing / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å | ||||||
![]() | Sosnowski, P. / Urnavicius, L. / Boland, A. / Fagiewicz, R. / Busselez, J. / Papai, G. / Schmidt, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The CryoEM structure of the ribosome maturation factor Rea1. Authors: Piotr Sosnowski / Linas Urnavicius / Andreas Boland / Robert Fagiewicz / Johan Busselez / Gabor Papai / Helgo Schmidt / ![]() ![]() Abstract: The biogenesis of 60S ribosomal subunits is initiated in the nucleus where rRNAs and proteins form pre-60S particles. These pre-60S particles mature by transiently interacting with various assembly ...The biogenesis of 60S ribosomal subunits is initiated in the nucleus where rRNAs and proteins form pre-60S particles. These pre-60S particles mature by transiently interacting with various assembly factors. The ~5000 amino-acid AAA+ ATPase Rea1 (or Midasin) generates force to mechanically remove assembly factors from pre-60S particles, which promotes their export to the cytosol. Here we present three Rea1 cryoEM structures. We visualise the Rea1 engine, a hexameric ring of AAA+ domains, and identify an α-helical bundle of AAA2 as a major ATPase activity regulator. The α-helical bundle interferes with nucleotide-induced conformational changes that create a docking site for the substrate binding MIDAS domain on the AAA +ring. Furthermore, we reveal the architecture of the Rea1 linker, which is involved in force generation and extends from the AAA+ ring. The data presented here provide insights into the mechanism of one of the most complex ribosome maturation factors. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 592.4 KB | Display | ![]() |
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PDB format | ![]() | 428.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 672.9 KB | Display | ![]() |
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Full document | ![]() | 707.9 KB | Display | |
Data in XML | ![]() | 86.7 KB | Display | |
Data in CIF | ![]() | 137.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0329MC ![]() 0308C ![]() 0309C ![]() 0328C ![]() 0330C ![]() 6hydC ![]() 6hypC ![]() 6i26C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 546538.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MDN1, REA1, YLR106C, L2901, L8004.13 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Rea1 (MIDASIN) AAA2L-H2alpha deletion mutant in AMPPNP State - electron density map Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.2 / Details: AMP-PNP was added 5 minute before the plunging | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 280 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 600 nm / Nominal defocus min: 500 nm / Cs: 0.01 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 12 mradians |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 46 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2479 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE / Spherical aberration corrector: Titan Krios Cs Corrector |
Image scans | Sampling size: 5 µm / Width: 3712 / Height: 3840 / Movie frames/image: 36 / Used frames/image: 2-36 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 201801 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20724 / Symmetry type: POINT |