Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Flexible Client-Dependent Cages in the Assembly Landscape of the Periplasmic Protease-Chaperone DegP.
Journal, issue, pages	J Am Chem Soc, Vol. 145, Issue 24, Page 13015-13026, Year 2023
Publish date	Jun 21, 2023
Authors	Robert W Harkness / Zev A Ripstein / Justin M Di Trani / Lewis E Kay /
PubMed Abstract	The periplasmic protein DegP, which is implicated in virulence factor transport leading to pathogenicity, is a bi-functional protease and chaperone that helps to maintain protein homeostasis in Gram- ...The periplasmic protein DegP, which is implicated in virulence factor transport leading to pathogenicity, is a bi-functional protease and chaperone that helps to maintain protein homeostasis in Gram-negative bacteria and is essential to bacterial survival under stress conditions. To perform these functions, DegP captures clients inside cage-like structures, which we have recently shown to form through the reorganization of high-order preformed apo oligomers, consisting of trimeric building blocks, that are structurally distinct from client-bound cages. Our previous studies suggested that these apo oligomers may allow DegP to encapsulate clients of various sizes under protein folding stresses by forming ensembles that can include extremely large cage particles, but how this occurs remains an open question. To explore the relation between cage and substrate sizes, we engineered a series of DegP clients of increasing hydrodynamic radii and analyzed their influence on DegP cage formation. We used dynamic light scattering and cryogenic electron microscopy to characterize the hydrodynamic properties and structures of the DegP cages that are adopted in response to each client. We present a series of density maps and structural models that include those for novel particles of approximately 30 and 60 monomers. Key interactions between DegP trimers and the bound clients that stabilize the cage assemblies and prime the clients for catalysis are revealed. We also provide evidence that DegP can form cages which approach subcellular organelles in terms of size.
External links	J Am Chem Soc / PubMed:37282495
Methods	EM (single particle)
Resolution	2.6 - 14.1 Å
Structure data	28754 8f0a EMDB-28754, PDB-8f0a: Client-bound structure of a DegP trimer within a 12mer cage Method: EM (single particle) / Resolution: 2.6 Å 28781 8f0u EMDB-28781, PDB-8f0u: Structure of a 12mer DegP cage bound to the client protein hTRF1 Method: EM (single particle) / Resolution: 3.1 Å 28800 8f1t EMDB-28800, PDB-8f1t: Structure of an 18mer DegP cage bound to the client protein hTRF1 Method: EM (single particle) / Resolution: 12.1 Å 28801 8f1u EMDB-28801, PDB-8f1u: Structure of a 24mer DegP cage bound to the client protein hTRF1 Method: EM (single particle) / Resolution: 13.8 Å 28806 8f21 EMDB-28806, PDB-8f21: Structure of a 30mer DegP cage bound to the client protein hTRF1 Method: EM (single particle) / Resolution: 14.1 Å 28808 8f26 EMDB-28808, PDB-8f26: Structure of a 60mer DegP cage bound to the client protein hTRF1 Method: EM (single particle) / Resolution: 9.7 Å
Source	escherichia coli (strain k12) (bacteria) homo sapiens (human)
Keywords	CHAPERONE / HYDROLASE / Protease / cage / complex