6OR6

Full-length S. pombe Mdn1 in the presence of AMPPNP (tail region)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis.

Chen, Z.Suzuki, H.Kobayashi, Y.Wang, A.C.DiMaio, F.Kawashima, S.A.Walz, T.Kapoor, T.M.

(2018) Cell 175: 822-834.e18

  • DOI: 10.1016/j.cell.2018.09.015
  • Primary Citation of Related Structures:  

  • PubMed 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 amino acid [aa]) and its limited homology to other we ...

    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.


    Organizational Affiliation

    Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA.,Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: kapoor@rockefeller.edu.,Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA. Electronic address: twalz@rockefeller.edu.,Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 1130033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Midasin
A
4717Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: mdn1
Find proteins for O94248 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94248
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM98579

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-12-18
    Type: Author supporting evidence, Other