|Entry||Database: PDB / ID: 6or5|
|Title||Full-length S. pombe Mdn1 in the presence of AMPPNP (ring region)|
|Keywords||MOTOR PROTEIN / Ribosome biogenesis / AAA protein / Mechanochemical enzyme / Ribosome assembly factor|
|Function / homology|
Function and homology information
preribosome, large subunit precursor / rRNA processing / ribosomal large subunit assembly / ATPase activity / nucleolus / calcium ion binding / nucleoplasm / ATP binding
ATPase, dynein-related, AAA domain / Midasin, AAA lid domain 7 / VWFA domain profile. / Midasin AAA lid domain / Midasin AAA lid domain / AAA domain (dynein-related subfamily) / von Willebrand factor, type A / AAA+ ATPase domain / Midasin AAA lid domain 5 / Midasin ...ATPase, dynein-related, AAA domain / Midasin, AAA lid domain 7 / VWFA domain profile. / Midasin AAA lid domain / Midasin AAA lid domain / AAA domain (dynein-related subfamily) / von Willebrand factor, type A / AAA+ ATPase domain / Midasin AAA lid domain 5 / Midasin / P-loop containing nucleoside triphosphate hydrolase / von Willebrand factor A-like domain superfamily
|Biological species||Schizosaccharomyces pombe (fission yeast)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å|
|Authors||Chen, Z. / Suzuki, H. / Wang, A.C. / DiMaio, F. / Walz, T. / Kapoor, T.M.|
|Funding support||United States , 1件 |
|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.
SummaryFull reportAbout validation report
|Date||Deposition: Apr 29, 2019 / Release: May 29, 2019|
|Structure viewer||Molecule: |
Downloads & links
|#1: Protein/peptide|| |
Mass: 538381.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: mdn1, SPCC737.08 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O94248
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: N-terminal density map of the full-length Mdn1 in the presence of AMPPNP|
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
|Molecular weight||Value: 0.54 MDa / Experimental value: NO|
|Source (natural)||Organism: Schizosaccharomyces pombe (fission yeast)|
|Source (recombinant)||Organism: Trichoplusia ni (cabbage looper)|
|Buffer solution||pH: 7.5|
|Specimen||Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µns|
|Specimen holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 15 sec. / Electron dose: 88.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8446|
|Image scans||Movie frames/image: 50 / Used frames/image: 1-50|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C1 (asymmetric)|
|3D reconstruction||Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 313336 / Symmetry type: POINT|
|Atomic model building||Protocol: FLEXIBLE FIT / Space: REAL|
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