5M43

Crystal structure of Yvh1 phosphatase domain from Chaetomium thermophilum

Summary for 5M43

• Entry DOI: 10.2210/pdb5m43/pdb
• Related: 5M3Q
• Descriptor: Putative uncharacterized protein, NITRATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: ribosome, phosphatase
• Biological source: Chaetomium thermophilum var. thermophilum DSM 1495
• Total number of polymer chains: 1
• Total formula weight: 25959.15

Authors

Ahmed, Y.L.,Sinning, I. (deposition date: 2016-10-18, release date: 2016-11-30, Last modification date: 2024-01-17)

Primary citation

Baler, J.,Ahmed, Y.L.,Kallas, M.,Kornprobst, M.,Calvino, F.R.,Gnadig, M.,Thoms, M.,Stier, G.,Ismail, S.,Kharde, S.,Castillo, N.,Griesel, S.,Bastuck, S.,Bradatsch, B.,Thomson, E.,Flemming, D.,Sinning, I.,Hurt, E.
Interaction network of the ribosome assembly machinery from a eukaryotic thermophile.
Protein Sci., 26:327-342, 2017

PubMed Abstract: Ribosome biogenesis in eukaryotic cells is a highly dynamic and complex process innately linked to cell proliferation. The assembly of ribosomes is driven by a myriad of biogenesis factors that shape pre-ribosomal particles by processing and folding the ribosomal RNA and incorporating ribosomal proteins. Biochemical approaches allowed the isolation and characterization of pre-ribosomal particles from Saccharomyces cerevisiae, which lead to a spatiotemporal map of biogenesis intermediates along the path from the nucleolus to the cytoplasm. Here, we cloned almost the entire set (∼180) of ribosome biogenesis factors from the thermophilic fungus Chaetomium thermophilum in order to perform an in-depth analysis of their protein-protein interaction network as well as exploring the suitability of these thermostable proteins for structural studies. First, we performed a systematic screen, testing about 80 factors for crystallization and structure determination. Next, we performed a yeast 2-hybrid analysis and tested about 32,000 binary combinations, which identified more than 1000 protein-protein contacts between the thermophilic ribosome assembly factors. To exemplary verify several of these interactions, we performed biochemical reconstitution with the focus on the interaction network between 90S pre-ribosome factors forming the ctUTP-A and ctUTP-B modules, and the Brix-domain containing assembly factors of the pre-60S subunit. Our work provides a rich resource for biochemical reconstitution and structural analyses of the conserved ribosome assembly machinery from a eukaryotic thermophile.

PubMed: 27863450
DOI: 10.1002/pro.3085

Experimental method

X-RAY DIFFRACTION (1.646 Å)