|Entry||Database: PDB / ID: 6ees|
|Title||Fitted model of S. pombe Mdn1 into the cryo-EM map obtained in the presence of ATP and Rbin-1|
|Keywords||MOTOR PROTEIN / Ribosome biogenesis / AAA protein / Mechanochemical enzyme / Ribosome assembly factor|
|Function / homology||Midasin AAA lid domain / ATPase, dynein-related, AAA domain / Midasin AAA lid domain / VWFA domain profile. / AAA domain (dynein-related subfamily) / von Willebrand factor A-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Midasin / AAA+ ATPase domain / von Willebrand factor, type A ...Midasin AAA lid domain / ATPase, dynein-related, AAA domain / Midasin AAA lid domain / VWFA domain profile. / AAA domain (dynein-related subfamily) / von Willebrand factor A-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Midasin / AAA+ ATPase domain / von Willebrand factor, type A / preribosome, large subunit precursor / rRNA processing / ribosomal large subunit assembly / ATPase activity / nucleolus / calcium ion binding / nucleoplasm / ATP binding / Midasin|
Function and homology information
|Specimen source||Schizosaccharomyces pombe (fission yeast)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.7 Å resolution|
|Authors||Chen, Z. / Suzuki, H. / Wang, A.C. / DiMaio, F. / Walz, T. / Kapoor, T.M.|
|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: Aug 15, 2018 / Release: Oct 17, 2018|
|Structure viewer||Molecule: |
Downloads & links
|#1: Protein/peptide|| |
Mass: 284556.188 Da / Num. of mol.: 1
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mdn1, SPCC737.08 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O94248
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: Full-length Mdn1 in the presence of ATP and Rbin-1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Value: 0.54 MDa / Experimental value: NO|
|Source (natural)||Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)|
Strain: 972 / ATCC 24843
|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: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3|
|Vitrification||Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 295 kelvins|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 28000 / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 15 sec. / Electron dose: 66.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 3887|
|Image scans||Movie frames/image: 50 / Used frames/image: 1-50|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 54557 / Symmetry type: POINT|
|Atomic model building||Ref protocol: RIGID BODY FIT / Ref space: REAL|
|Atomic model building||PDB-ID: 6EDO|
Pdb chain ID: A / Pdb chain residue range: 2-2383
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