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Motor mechanism for protein threading through Hsp104.

Molecular cell | Apr 10, 2009

The protein-remodeling machine Hsp104 dissolves amorphous aggregates as well as ordered amyloid assemblies such as yeast prions. Force generation originates from a tandem AAA+ (ATPases associated with various cellular activities) cassette, but the mechanism and allostery of this action remain to be established. Our cryoelectron microscopy maps of Hsp104 hexamers reveal substantial domain movements upon ATP binding and hydrolysis in the first nucleotide-binding domain (NBD1). Fitting atomic models of Hsp104 domains to the EM density maps plus supporting biochemical measurements show how the domain movements displace sites bearing the substrate-binding tyrosine loops. This provides the structural basis for N- to C-terminal substrate threading through the central cavity, enabling a clockwise handover of substrate in the NBD1 ring and coordinated substrate binding between NBD1 and NBD2. Asymmetric reconstructions of Hsp104 in the presence of ATPgammaS or ATP support sequential rather than concerted ATP hydrolysis in the NBD1 ring.

Pubmed ID: 19362537 RIS Download

Mesh terms: Adenosine Triphosphate | Amino Acid Motifs | Cryoelectron Microscopy | Heat-Shock Proteins | Hydrolysis | Imaging, Three-Dimensional | Models, Molecular | Protein Structure, Tertiary | Saccharomyces cerevisiae Proteins | Substrate Specificity

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PyMOL

A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.

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EMDataBank.org: Unified Data Resource for Cryo Electron Microscopy

A unified global portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata, as well as a resource for news, events, software tools, data standards, validation methods for the 3DEM community. It is a joint effort among investigators of the Protein Databank in Europe (PDBe) at the European Bioinformatics Institute, the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, and the National Center for Macromolecular Imaging (NCMI) at Baylor College of Medicine. A major goal of the EMDataBank project in their current funding period is to work with the 3DEM community to (1) establish data-validation methods that can be used in the process of structure determination, (2) define the key indicators of a well-determined structure that should accompany every deposition, and (3) implement appropriate validation procedures for maps and map-derived models into a 3DEM validation pipeline. The EM Validation Task Force (EM VTF) has made initial recommendations to guide development of 3DEM validation criteria. Their aim is to facilitate the many processes needed to assess, establish, and disseminate validation methods and standards. The Web Service allows other applications to obtain data regarding maps/structures in the EMDB. The data is returned in XML format.

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