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	23S rRNA modifications stimulate catalytic activity and prevent the formation of alternative structures.
Journal, issue, pages	Nucleic Acids Res, Vol. 54, Issue 15, Year 2026
Publish date	Aug 10, 2026
Authors	Daniel S D Larsson / Aivar Liiv / Rya Ero / Jaanus Remme / Maria Selmer /
PubMed Abstract	Ribosomal RNA (rRNA) modifications cluster around the peptidyl transferase centre (PTC), the catalytic centre of the ribosome, yet their collective functional roles remain unclear. Here we analyse ...Ribosomal RNA (rRNA) modifications cluster around the peptidyl transferase centre (PTC), the catalytic centre of the ribosome, yet their collective functional roles remain unclear. Here we analyse Escherichia coli ribosomes lacking 11 or 12 modifications near the PTC. Using kinetic assays, we show these hypo-modified ribosomes catalyse peptide bond formation at rates twofold to threefold lower than wild-type and exhibit reduced thermal stability. Cryo-electron microscopy of hypo-modified ribosomes reveals multiple alternative conformations of the PTC and exit tunnel regions, disrupting native stacking and hydrogen bonding critical for positioning of transfer RNA substrates. These findings indicate that rRNA modifications stabilize the native PTC structure, preventing formation of alternative, nonfunctional conformations and thereby enhancing catalytic efficiency. Our study provides insight into how rRNA modifications fine-tune ribosome function by maintaining structural integrity essential for efficient translation.
External links	Nucleic Acids Res / PubMed:42598854 / PubMed Central
Methods	EM (single particle)
Resolution	1.87 - 3.07 Å
Structure data	55349 9syh EMDB-55349, PDB-9syh: E. coli 70S ribosome from deltaRlmE strain Method: EM (single particle) / Resolution: 1.89 Å 55415 9t0y EMDB-55415, PDB-9t0y: E. coli 70S ribosome from delta-9 strain Method: EM (single particle) / Resolution: 1.87 Å 55427 9t19 EMDB-55427, PDB-9t19: E. coli 70S ribosome from delta-RlmE strain, PTC class 0 Method: EM (single particle) / Resolution: 2.41 Å 55428 9t1a EMDB-55428, PDB-9t1a: E. coli 70S ribosome from delta-RlmE strain, PTC class 1 Method: EM (single particle) / Resolution: 2.39 Å 55429 9t1b EMDB-55429, PDB-9t1b: E. coli 70S ribosome from delta-RlmE strain, PTC class 2 Method: EM (single particle) / Resolution: 2.32 Å 55430 9t1c EMDB-55430, PDB-9t1c: E. coli 70S ribosome from delta-RlmE strain, PTC class 3 Method: EM (single particle) / Resolution: 3.07 Å 55432 9t1e EMDB-55432, PDB-9t1e: E. coli 70S ribosome from delta-RlmE strain, PTC class 4 Method: EM (single particle) / Resolution: 2.28 Å 55433 9t1f EMDB-55433, PDB-9t1f: E. coli 70S ribosome from delta-RlmE strain, PTC class 5 Method: EM (single particle) / Resolution: 2.32 Å 55434 9t1g EMDB-55434, PDB-9t1g: E. coli 70S ribosome from delta-RlmE strain, PTC class 6 Method: EM (single particle) / Resolution: 2.29 Å 55435 9t1h EMDB-55435, PDB-9t1h: E. coli 70S ribosome from delta-RlmE strain, PTC class 7 Method: EM (single particle) / Resolution: 2.33 Å 55436 9t1i EMDB-55436, PDB-9t1i: E. coli 70S ribosome from delta-RlmE strain, PTC class 8 Method: EM (single particle) / Resolution: 2.3 Å 55437 9t1j EMDB-55437, PDB-9t1j: E. coli 70S ribosome from delta-RlmE strain, PTC class 9 Method: EM (single particle) / Resolution: 2.23 Å 55467 9t2j EMDB-55467, PDB-9t2j: E. coli 70S ribosome from delta-9 strain, PTC class 0 Method: EM (single particle) / Resolution: 2.02 Å 55468 9t2k EMDB-55468, PDB-9t2k: E. coli 70S ribosome from delta-9 strain, PTC class 1 Method: EM (single particle) / Resolution: 2.06 Å 55469 9t2l EMDB-55469, PDB-9t2l: E. coli 70S ribosome from delta-9 strain, PTC class 2 Method: EM (single particle) / Resolution: 2.07 Å 55470 9t2m EMDB-55470, PDB-9t2m: E. coli 70S ribosome from delta-9 strain, PTC class 3 Method: EM (single particle) / Resolution: 2.06 Å 55471 9t2n EMDB-55471, PDB-9t2n: E. coli 70S ribosome from delta-9 strain, PTC class 4 Method: EM (single particle) / Resolution: 2.06 Å 55472 9t2o EMDB-55472, PDB-9t2o: E. coli 70S ribosome from delta-9 strain, PTC class 5 Method: EM (single particle) / Resolution: 2.07 Å 55473 9t2p EMDB-55473, PDB-9t2p: E. coli 70S ribosome from delta-9 strain, PTC class 6 Method: EM (single particle) / Resolution: 2.08 Å 55474 9t2q EMDB-55474, PDB-9t2q: E. coli 70S ribosome from delta-9 strain, PTC class 7 Method: EM (single particle) / Resolution: 2.08 Å 55475 9t2r EMDB-55475, PDB-9t2r: E. coli 70S ribosome from delta-9 strain, PTC class 8 Method: EM (single particle) / Resolution: 2.22 Å 55476 9t2s EMDB-55476, PDB-9t2s: E. coli 70S ribosome from delta-9 strain, PTC class 9 Method: EM (single particle) / Resolution: 2.07 Å 55618 9t6m EMDB-55618, PDB-9t6m: E. coli 70S ribosome from delta-10 strain Method: EM (single particle) / Resolution: 1.87 Å 55702 9t8k EMDB-55702, PDB-9t8k: E. coli 70S ribosome from delta-10 strain, PTC class 0 Method: EM (single particle) / Resolution: 2.18 Å 55703 9t8l EMDB-55703, PDB-9t8l: E. coli 70S ribosome from delta-10 strain, PTC class 1 Method: EM (single particle) / Resolution: 2.21 Å 55704 9t8m EMDB-55704, PDB-9t8m: E. coli 70S ribosome from delta-10 strain, PTC class 2 Method: EM (single particle) / Resolution: 2.2 Å 55705 9t8n EMDB-55705, PDB-9t8n: E. coli 70S ribosome from delta-10 strain, PTC class 3 Method: EM (single particle) / Resolution: 2.22 Å 55706 9t8o EMDB-55706, PDB-9t8o: E. coli 70S ribosome from delta-10 strain, PTC class 4 Method: EM (single particle) / Resolution: 2.19 Å 55707 9t8p EMDB-55707, PDB-9t8p: E. coli 70S ribosome from delta-10 strain, PTC class 5 Method: EM (single particle) / Resolution: 2.22 Å 55708 9t8q EMDB-55708, PDB-9t8q: E. coli 70S ribosome from delta-10 strain, PTC class 6 Method: EM (single particle) / Resolution: 2.23 Å 55711 9t8t EMDB-55711, PDB-9t8t: E. coli 70S ribosome from delta-10 strain, PTC class 9 Method: EM (single particle) / Resolution: 2.23 Å
Chemicals	ChemComp-K: Unknown entry ChemComp-MG: Unknown entry ChemComp-SR0: N~1~-(3-azaniumylpropyl)butane-1,4-diaminium ChemComp-PUT: 1,4-DIAMINOBUTANE ChemComp-ZN: Unknown entry ChemComp-HOH: WATER
Source	escherichia coli (E. coli)
Keywords	RIBOSOME / RNA modifications / ribosome biogenesis / maturation