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
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Journal
IF	>30 >20 >10 >5 all

Title	Mechanism of release factor-mediated peptidyl-tRNA hydrolysis on the ribosome.
Journal, issue, pages	Science, Vol. 388, Issue 6753, Page eads9030, Year 2025
Publish date	Jun 19, 2025
Authors	Elena V Aleksandrova / Egor A Syroegin / Ritwika S Basu / Alexander A Vassilevski / Matthieu G Gagnon / Yury S Polikanov /
PubMed Abstract	Translation termination is essential in all living organisms because it ensures that proteins have lengths strictly defined by their genes. This universal process is mediated by peptide release ...Translation termination is essential in all living organisms because it ensures that proteins have lengths strictly defined by their genes. This universal process is mediated by peptide release factors (RFs) that recognize stop codons and catalyze the hydrolysis of peptidyl transfer RNA (peptidyl-tRNA) on the ribosome, presumably by activating a water molecule. We report structures of the bacterial ribosome in complex with peptidyl-tRNA and RFs in the prepeptide release state. No hydrolytic water molecule was seen in the peptidyl transferase center. Instead, RFs induced rearrangements of the peptidyl-tRNA adenine 76 (A76) ribose pucker that orient the 2'-OH for the nucleophilic attack onto the neighboring carbonyl group. These findings suggest a catalytic mechanism of RF-mediated peptide release and provide a structural basis for the universal conservation of the catalytic domain in peptide RFs.
External links	Science / PubMed:40536958
Methods	EM (single particle) / X-ray diffraction
Resolution	2.13 - 2.8 Å
Structure data	49594 9no7 EMDB-49594, PDB-9no7: Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q230-N5-methylated Release Factor 1, and P-site 2'-deoxy-A76-fMEAAAKC-peptidyl-tRNAcys at 2.13A resolution Method: EM (single particle) / Resolution: 2.13 Å PDB-9mtp: Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q230-N5-methylated Release Factor 1, and P-site fMEAAAKC-peptidyl-tRNAcys at 2.40A resolution Method: X-RAY DIFFRACTION / Resolution: 2.4 Å PDB-9mtq: Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site GGD-mutant Release Factor 1, and P-site fMEAAAKC-peptidyl-tRNAcys at 2.55A resolution Method: X-RAY DIFFRACTION / Resolution: 2.55 Å PDB-9mtr: Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site GGS-mutant Release Factor 1, and P-site fMEAAAKC-peptidyl-tRNAcys at 2.80A resolution Method: X-RAY DIFFRACTION / Resolution: 2.8 Å PDB-9mts: Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q230-unmodified Release Factor 1, and P-site fMEAAAKC-peptidyl-tRNAcys at 2.70A resolution Method: X-RAY DIFFRACTION / Resolution: 2.7 Å PDB-9mtt: Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q230-N5-methylated Release Factor 1, and P-site deacylated-tRNAcys at 2.60A resolution Method: X-RAY DIFFRACTION / Resolution: 2.6 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-K: Unknown entry ChemComp-ZN: Unknown entry ChemComp-SF4: IRON/SULFUR CLUSTER ChemComp-HOH: WATER
Source	thermus thermophilus (bacteria) thermus thermophilus hb8 (bacteria) escherichia coli (E. coli) escherichia phage t4 (virus)
Keywords	RIBOSOME / Translation termination; peptide release; release factor; hydrolysis; peptidyl-tRNA; non-hydrolyzable; 70S ribosome; X-ray structure; pre-termination state; peptidyl transferase center / Translation termination; peptide release; release factor; hydrolysis; peptidyl-tRNA; 70S ribosome; cryo-EM; pre-termination state; peptidyl transferase center