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	Assembly of the bacterial ribosome with circularly permuted rRNA.
Journal, issue, pages	Nucleic Acids Res, Vol. 52, Issue 18, Page 11254-11265, Year 2024
Publish date	Oct 14, 2024
Authors	Xiyu Dong / Kai Sheng / Luca F R Gebert / Sriram Aiyer / Ian J MacRae / Dmitry Lyumkis / James R Williamson /
PubMed Abstract	Co-transcriptional assembly is an integral feature of the formation of RNA-protein complexes that mediate translation. For ribosome synthesis, prior studies have indicated that the strict order of ...Co-transcriptional assembly is an integral feature of the formation of RNA-protein complexes that mediate translation. For ribosome synthesis, prior studies have indicated that the strict order of transcription of rRNA domains may not be obligatory during bacterial ribosome biogenesis, since a series of circularly permuted rRNAs are viable. In this work, we report the structural insights into assembly of the bacterial ribosome large subunit (LSU) based on cryo-EM density maps of intermediates that accumulate during in vitro ribosome synthesis using a set of circularly permuted (CiPer) rRNAs. The observed ensemble of 23 resolved ribosome large subunit intermediates reveals conserved assembly routes with an underlying hierarchy among cooperative assembly blocks. There are intricate interdependencies for the formation of key structural rRNA helices revealed from the circular permutation of rRNA. While the order of domain synthesis is not obligatory, the order of domain association does appear to proceed with a particular order, likely due to the strong evolutionary pressure on efficient ribosome synthesis. This work reinforces the robustness of the known assembly hierarchy of the bacterial large ribosomal subunit and offers a coherent view of how efficient assembly of CiPer rRNAs can be understood in that context.
External links	Nucleic Acids Res / PubMed:39036963 / PubMed Central
Methods	EM (single particle)
Resolution	4.8 - 8.7 Å
Structure data	EMDB-43844: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP45 Class B Method: EM (single particle) / Resolution: 6.3 Å EMDB-43845: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP45 Class C1 Method: EM (single particle) / Resolution: 6.4 Å EMDB-43846: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP45 Class C2 Method: EM (single particle) / Resolution: 4.8 Å EMDB-43847: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP45 Class E2 Method: EM (single particle) / Resolution: 4.8 Å EMDB-43848: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP45 Class G Method: EM (single particle) / Resolution: 6.8 Å EMDB-43849: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP45 Class E1 Method: EM (single particle) / Resolution: 6.7 Å EMDB-43850: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63 Class C Method: EM (single particle) / Resolution: 5.2 Å EMDB-43851: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63 Class E2 Method: EM (single particle) / Resolution: 4.9 Å EMDB-43852: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63 Class E1 Method: EM (single particle) / Resolution: 5.7 Å EMDB-43853: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63 Class D Method: EM (single particle) / Resolution: 6.7 Å EMDB-43854: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63 Class B Method: EM (single particle) / Resolution: 7.0 Å EMDB-43856: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63(+PS) Class E Method: EM (single particle) / Resolution: 5.3 Å EMDB-43857: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63(+PS) Class C2 Method: EM (single particle) / Resolution: 5.8 Å EMDB-43858: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63(+PS) Class B Method: EM (single particle) / Resolution: 7.1 Å EMDB-43859: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63(+PS) Class C3 Method: EM (single particle) / Resolution: 6.9 Å EMDB-43860: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63(+PS) Class D1 Method: EM (single particle) / Resolution: 8.6 Å EMDB-43861: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63(+PS) Class C1 Method: EM (single particle) / Resolution: 8.1 Å EMDB-43862: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63(+PS) Class C4 Method: EM (single particle) / Resolution: 7.3 Å EMDB-43863: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP63(+PS) Class D2 Method: EM (single particle) / Resolution: 8.7 Å EMDB-43864: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP78 Class B Method: EM (single particle) / Resolution: 8.7 Å EMDB-43865: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP78 Class C1 Method: EM (single particle) / Resolution: 8.0 Å EMDB-43866: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP78 Class C2 Method: EM (single particle) / Resolution: 8.0 Å EMDB-43867: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP78 Class C3 Method: EM (single particle) / Resolution: 5.6 Å
Source	Escherichia coli (E. coli)