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	Cryo-EM structure and rRNA modification sites of a plant ribosome.
Journal, issue, pages	Plant Commun, Vol. 3, Issue 5, Page 100342, Year 2022
Publish date	Sep 12, 2022
Authors	Patrick Cottilli / Yuzuru Itoh / Yuko Nobe / Anton S Petrov / Purificación Lisón / Masato Taoka / Alexey Amunts /
PubMed Abstract	Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to ...Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.
External links	Plant Commun / PubMed:35643637 / PubMed Central
Methods	EM (single particle)
Resolution	2.35 - 2.8 Å
Structure data	14001 7qiw EMDB-14001, PDB-7qiw: Specific features and methylation sites of a plant ribosome. 60S ribosomal subunit. Method: EM (single particle) / Resolution: 2.35 Å 14002 7qix EMDB-14002, PDB-7qix: Specific features and methylation sites of a plant ribosome. 40S body ribosomal subunit. Method: EM (single particle) / Resolution: 2.53 Å 14003 7qiy EMDB-14003: Specific features and methylation sites of a plant ribosome PDB-7qiy: Specific features and methylation sites of a plant ribosome. 40S head ribosomal subunit. Method: EM (single particle) / Resolution: 2.58 Å 14004 7qiz EMDB-14004, PDB-7qiz: Specific features and methylation sites of a plant 80S ribosome Method: EM (single particle) / Resolution: 2.38 Å EMDB-14051: Specific features and methylation sites of a plant ribosome. 80S translating ribosome (A/A-P/P-E/E). Method: EM (single particle) / Resolution: 2.8 Å EMDB-14052: Specific features and methylation sites of a plant ribosome. 80S translating ribosome (A/P-P/E). Method: EM (single particle) / Resolution: 2.7 Å EMDB-32404: Specific features and methylation sites of a plant ribosome. 80S ribosome consensus map. Method: EM (single particle) / Resolution: 2.38 Å
Chemicals	ChemComp-K: Unknown entry ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-SPM: SPERMINE / Spermine ChemComp-SPD: SPERMIDINE / Spermidine ChemComp-HOH: WATER / Water ChemComp-PUT: 1,4-DIAMINOBUTANE / Putrescine ChemComp-BGC: beta-D-glucopyranose / Glucose
Source	solanum lycopersicum (tomato)
Keywords	RIBOSOME / Solanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA