+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0330 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Rea1 Wild type ADP state (AAA+ ring + stem) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Sosnowski P / Urnavicius L / Boland A / Fagiewicz R / Busselez J / Papai G / Schmidt H | |||||||||
Funding support | France, 1 items
| |||||||||
Citation | Journal: Elife / Year: 2018 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0330.map.gz | 184.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0330-v30.xml emd-0330.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0330_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_0330.png | 34 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0330 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0330 | HTTPS FTP |
-Related structure data
Related structure data | 0308C 0309C 0328C 0329C 6hydC 6hypC 6i26C 6i27C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_0330.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Rea1 (MIDASIN) ring with ADP
Entire | Name: Rea1 (MIDASIN) ring with ADP |
---|---|
Components |
|
-Supramolecule #1: Rea1 (MIDASIN) ring with ADP
Supramolecule | Name: Rea1 (MIDASIN) ring with ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.2 Component:
Details: ADP was added 5 minute before the plunging | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 105000 |
Specialist optics | Spherical aberration corrector: Titan Krios Cs Corrector / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3712 pixel / Digitization - Dimensions - Height: 3840 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 2-35 / Number grids imaged: 14 / Number real images: 23230 / Average exposure time: 0.2 sec. / Average electron dose: 46.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |