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Yorodumi- PDB-7qiw: Specific features and methylation sites of a plant ribosome. 60S ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qiw | |||||||||||||||
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Title | Specific features and methylation sites of a plant ribosome. 60S ribosomal subunit. | |||||||||||||||
Components |
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Keywords | RIBOSOME / Solanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA | |||||||||||||||
Function / homology | Function and homology information protein-RNA complex assembly / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / modification-dependent protein catabolic process / protein tag activity / large ribosomal subunit / ribosome biogenesis / large ribosomal subunit rRNA binding / 5S rRNA binding ...protein-RNA complex assembly / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / modification-dependent protein catabolic process / protein tag activity / large ribosomal subunit / ribosome biogenesis / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Solanum lycopersicum (tomato) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å | |||||||||||||||
Authors | Cottilli, P. / Itoh, Y. / Amunts, A. | |||||||||||||||
Funding support | European Union, 4items
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Citation | Journal: Plant Commun / Year: 2022 Title: Cryo-EM structure and rRNA modification sites of a plant ribosome. Authors: Patrick Cottilli / Yuzuru Itoh / Yuko Nobe / Anton S Petrov / Purificación Lisón / Masato Taoka / Alexey Amunts / 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. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qiw.cif.gz | 4.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7qiw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qiw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7qiw_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7qiw_validation.xml.gz | 202.9 KB | Display | |
Data in CIF | 7qiw_validation.cif.gz | 372.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/7qiw ftp://data.pdbj.org/pub/pdb/validation_reports/qi/7qiw | HTTPS FTP |
-Related structure data
Related structure data | 14001MC 7qixC 7qiyC 7qizC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+60S ribosomal protein ... , 21 types, 21 molecules DKLMNQUVWXbdfghikmnpq
-Protein , 14 types, 14 molecules FGHIORSYZacjor
#2: Protein | Mass: 44852.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HW81 |
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#4: Protein | Mass: 34667.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7H274 |
#5: Protein | Mass: 25621.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GMA5 |
#6: Protein | Mass: 28057.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: M1BRF8 |
#12: Protein | Mass: 15400.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7J0J5 |
#15: Protein | Mass: 19785.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FNQ5 |
#16: Protein | Mass: 20764.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7I5W4 |
#22: Protein | Mass: 18712.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7IN69 |
#23: Protein | Mass: 17427.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7INK3 |
#24: Protein | Mass: 16750.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: MKYNPRVSSSRRKSRKAHFTAPSSLRRVLMSAPLSSELRAKYSVRSMPVRKDDEVQVVRG TYKGREGKVVQVYRKKWVIHIERITREKVNGSTVNVGIHPSKVVISKLRLDKDRRSLLDR KAKGRAAADKDKGTKFTTEEIMQAID Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FBC6 |
#26: Protein | Mass: 16479.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A0V0H357 |
#33: Protein | Mass: 14324.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: Q53U38 |
#38: Protein | Mass: 14745.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4B017 |
#41: Protein | Mass: 16018.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FVJ9 |
-Ribosomal protein ... , 4 types, 4 molecules EPTl
#3: Protein | Mass: 44518.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: Q6SKP4 |
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#13: Protein | Mass: 24233.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HQH0 |
#17: Protein | Mass: 24786.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GQ29 |
#35: Protein | Mass: 10809.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FV98 |
-Ribosomal L7Ae domain-containing ... , 2 types, 2 molecules Je
#7: Protein | Mass: 29362.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GV73 |
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#28: Protein | Mass: 12367.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7E9D6 |
-RNA chain , 4 types, 4 molecules s258
#42: RNA chain | Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) |
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#43: RNA chain | Mass: 1098453.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: GenBank: 2090998066 |
#44: RNA chain | Mass: 38634.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: GenBank: 19159 |
#45: RNA chain | Mass: 53173.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: GenBank: 1418500722 |
-Non-polymers , 6 types, 4309 molecules
#46: Chemical | ChemComp-K / #47: Chemical | ChemComp-MG / #48: Chemical | ChemComp-ZN / #49: Chemical | #50: Chemical | ChemComp-SPD / | #51: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 60S ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#45 / Source: NATURAL |
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Source (natural) | Organism: Solanum lycopersicum (tomato) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 30.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: (1.19.2_4158:phenix.real_space_refine) / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335806 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: THROUGHOUT | ||||||||||||||||||||||||
Displacement parameters | Biso max: 77.84 Å2 / Biso mean: 13.508 Å2 / Biso min: 0.04 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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