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	A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.
Journal, issue, pages	Sci Adv, Vol. 7, Issue 23, Year 2021
Publish date	Jun 4, 2021
Authors	Andreas Schedlbauer / Idoia Iturrioz / Borja Ochoa-Lizarralde / Tammo Diercks / Jorge Pedro López-Alonso / José Luis Lavin / Tatsuya Kaminishi / Retina Çapuni / Neha Dhimole / Elisa de Astigarraga / David Gil-Carton / Paola Fucini / Sean R Connell /
PubMed Abstract	While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high- ...While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30 ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16 ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
External links	Sci Adv / PubMed:34088665 / PubMed Central
Methods	EM (single particle) / NMR (solution)
Resolution	2.75 - 4.9 Å
Structure data	11751 7af3 EMDB-11751, PDB-7af3: Bacterial 30S ribosomal subunit assembly complex state M (head domain) Method: EM (single particle) / Resolution: 2.82 Å 11753 7af5 EMDB-11753, PDB-7af5: Bacterial 30S ribosomal subunit assembly complex state I (head domain) Method: EM (single particle) / Resolution: 2.96 Å 11756 7af8 EMDB-11756, PDB-7af8: Bacterial 30S ribosomal subunit assembly complex state E (head domain) Method: EM (single particle) / Resolution: 2.75 Å 11758 7afa EMDB-11758, PDB-7afa: Bacterial 30S ribosomal subunit assembly complex state F (head domain) Method: EM (single particle) / Resolution: 2.95 Å 11761 7afd EMDB-11761, PDB-7afd: Bacterial 30S ribosomal subunit assembly complex state A (head domain) Method: EM (single particle) / Resolution: 3.44 Å 11765 7afh EMDB-11765, PDB-7afh: Bacterial 30S ribosomal subunit assembly complex state C (head domain) Method: EM (single particle) / Resolution: 3.59 Å 11766 7afi EMDB-11766, PDB-7afi: Bacterial 30S ribosomal subunit assembly complex state C (body domain) Method: EM (single particle) / Resolution: 3.53 Å 11768 7afk EMDB-11768, PDB-7afk: Bacterial 30S ribosomal subunit assembly complex state D (head domain) Method: EM (single particle) / Resolution: 4.9 Å 11769 7afl EMDB-11769, PDB-7afl: Bacterial 30S ribosomal subunit assembly complex state D (multibody refinement for body domain of 30S ribosome) Method: EM (single particle) / Resolution: 4.2 Å 11771 7afn EMDB-11771, PDB-7afn: Bacterial 30S ribosomal subunit assembly complex state B (head domain) Method: EM (single particle) / Resolution: 3.86 Å 11772 7afo EMDB-11772, PDB-7afo: Bacterial 30S ribosomal subunit assembly complex state B (body domain) Method: EM (single particle) / Resolution: 3.93 Å 12239 7bod EMDB-12239, PDB-7bod: Bacterial 30S ribosomal subunit assembly complex state M (body domain) Method: EM (single particle) / Resolution: 2.88 Å 12240 7boe EMDB-12240, PDB-7boe: Bacterial 30S ribosomal subunit assembly complex state M (Consensus refinement) Method: EM (single particle) / Resolution: 2.9 Å 12241 7bof EMDB-12241, PDB-7bof: Bacterial 30S ribosomal subunit assembly complex state I (body domain) Method: EM (single particle) / Resolution: 2.92 Å 12242 7bog EMDB-12242, PDB-7bog: Bacterial 30S ribosomal subunit assembly complex state E (body domain) Method: EM (single particle) / Resolution: 2.75 Å 12243 7boh EMDB-12243, PDB-7boh: Complete Bacterial 30S ribosomal subunit assembly complex state E (+RbfA)(Consensus Refinement) Method: EM (single particle) / Resolution: 2.82 Å 12244 7boi EMDB-12244, PDB-7boi: Bacterial 30S ribosomal subunit assembly complex state F (multibody refinement for body domain of 30S ribosome) Method: EM (single particle) / Resolution: 2.98 Å 12245 7nar EMDB-12245, PDB-7nar: Complete Bacterial 30S ribosomal subunit assembly complex state F (+RsgA)(Consensus Refinement) Method: EM (single particle) / Resolution: 3.0 Å 12246 7nas EMDB-12246, PDB-7nas: Bacterial 30S ribosomal subunit assembly complex state A (multibody refinement for body domain of 30S ribosome) Method: EM (single particle) / Resolution: 3.31 Å 12247 7nat EMDB-12247, PDB-7nat: Bacterial 30S ribosomal subunit assembly complex state A (Consensus refinement) Method: EM (single particle) / Resolution: 3.59 Å 12248 7nau EMDB-12248, PDB-7nau: Bacterial 30S ribosomal subunit assembly complex state C (Consensus Refinement) Method: EM (single particle) / Resolution: 3.78 Å 12249 7nav EMDB-12249, PDB-7nav: Bacterial 30S ribosomal subunit assembly complex state D (Consensus refinement) Method: EM (single particle) / Resolution: 4.8 Å 12251 7nax EMDB-12251, PDB-7nax: Complete Bacterial 30S ribosomal subunit assembly complex state I (Consensus Refinement) Method: EM (single particle) / Resolution: 2.96 Å PDB-7afq: Ribosome binding factor A (RbfA) Method: SOLUTION NMR PDB-7afr: Ribosome maturation factor RimP (apo) Method: SOLUTION NMR
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate
Source	escherichia coli (E. coli) escherichia coli (strain k12) (bacteria) escherichia coli k-12 (bacteria) escherichia coli o26:h11 (bacteria)
Keywords	RIBOSOME / Cryo-EM / 30S biogenesis / ribosome assembly / RbfA / RsgA / YjeQ / RimP / KsgA / RsmA / RNA BINDING PROTEIN / Solution state NMR / RbfA. / RimP.