|Entry||Database: EMDB / ID: 9034|
|Title||C-terminally truncated S. pombe Mdn1 (1-3911 aa) in the presence of AMPPNP (ring region)|
|Map data||C-terminally truncated S. pombe Mdn1 (1-3911 aa) in the presence of AMPPNP (ring region), primary map|
|Sample||N-terminal density map of the C-terminally truncated Mdn1 in the presence of AMPPNP:|
|Source||Schizosaccharomyces pombe (fission yeast)|
|Method||single particle reconstruction / cryo EM / 6.1 Å resolution|
|Authors||Chen Z / Suzuki H / Wang AC / DiMaio F / Walz T / Kapoor TM|
|Citation||Journal: Cell / Year: 2018|
Title: Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis.
Authors: Zhen Chen / Hiroshi Suzuki / Yuki Kobayashi / Ashley C Wang / Frank DiMaio / Shigehiro A Kawashima / Thomas Walz / Tarun M Kapoor
Abstract: Mdn1 is an essential AAA (ATPase associated with various activities) protein that removes assembly factors from distinct precursors of the ribosomal 60S subunit. However, Mdn1's large size (∼5,000 ...Mdn1 is an essential AAA (ATPase associated with various activities) protein that removes assembly factors from distinct precursors of the ribosomal 60S subunit. However, Mdn1's large size (∼5,000 amino acid [aa]) and its limited homology to other well-studied proteins have restricted our understanding of its remodeling function. Here, we present structures for S. pombe Mdn1 in the presence of AMPPNP at up to ∼4 Å or ATP plus Rbin-1, a chemical inhibitor, at ∼8 Å resolution. These data reveal that Mdn1's MIDAS domain is tethered to its ring-shaped AAA domain through an ∼20 nm long structured linker and a flexible ∼500 aa Asp/Glu-rich motif. We find that the MIDAS domain, which also binds other ribosome-assembly factors, docks onto the AAA ring in a nucleotide state-specific manner. Together, our findings reveal how conformational changes in the AAA ring can be directly transmitted to the MIDAS domain and thereby drive the targeted release of assembly factors from ribosomal 60S-subunit precursors.
|Date||Deposition: Aug 9, 2018 / Header (metadata) release: Aug 29, 2018 / Map release: Oct 17, 2018 / Last update: Oct 31, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_9034.map.gz (map file in CCP4 format, 108001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.3 Å|
CCP4 map header:
-Entire N-terminal density map of the C-terminally truncated Mdn1 in the ...
|Entire||Name: N-terminal density map of the C-terminally truncated Mdn1 in the presence of AMPPNP|
Number of components: 1
-Component #1: cellular-component, N-terminal density map of the C-terminally tr...
|Cellular-component||Name: N-terminal density map of the C-terminally truncated Mdn1 in the presence of AMPPNP|
Recombinant expression: No
|Mass||Theoretical: 450 kDa|
|Source||Species: Schizosaccharomyces pombe (fission yeast)|
|Source (engineered)||Expression System: Trichoplusia ni (cabbage looper)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.15 mg/ml / pH: 7.5|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 88.8 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 22500.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400.0 - 3000.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 2745|
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