+Open data
-Basic information
Entry | Database: PDB / ID: 7qiz | |||||||||||||||
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Title | Specific features and methylation sites of a plant 80S ribosome | |||||||||||||||
Components |
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Keywords | RIBOSOME / Solanum lycopersicum / cytosolic ribosome / 80S / plant / rRNA | |||||||||||||||
Function / homology | Function and homology information pectinesterase / : / pectinesterase activity / cell wall modification / pectin catabolic process / MAP kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...pectinesterase / : / pectinesterase activity / cell wall modification / pectin catabolic process / MAP kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / intracellular signal transduction / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Solanum lycopersicum (tomato) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 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 | 7qiz.cif.gz | 7.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7qiz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qiz_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7qiz_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7qiz_validation.xml.gz | 301.6 KB | Display | |
Data in CIF | 7qiz_validation.cif.gz | 552 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/7qiz ftp://data.pdbj.org/pub/pdb/validation_reports/qi/7qiz | HTTPS FTP |
-Related structure data
Related structure data | 14004MC 7qiwC 7qixC 7qiyC C: citing same article (ref.) M: map data used to model this data |
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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 ... , 22 types, 22 molecules DKLMNUVWXbdefghikmnpqt
+Protein , 22 types, 22 molecules FGHIJOQRYZajorNAOAPAVAYAzEAHA
-Ribosomal protein ... , 5 types, 5 molecules EPTlIA
#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 |
#76: Protein | Mass: 16389.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: Q38JI8 |
-Ribosomal L18e/L15P domain-containing ... , 2 types, 2 molecules Sc
#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 |
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#26: Protein | Mass: 16479.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GZ10 |
-RNA chain , 7 types, 7 molecules s258S2aAbA
#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 |
#46: RNA chain | Mass: 583609.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) |
#59: RNA chain | Mass: 4470.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) |
#60: RNA chain | Mass: 895.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) |
-40S ribosomal protein ... , 20 types, 20 molecules QARATAUAWAXAZAuvwxyAABADAFAKALAMAJA
#50: Protein | Mass: 17352.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7F5X2 |
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#51: Protein | Mass: 16805.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GDB0 |
#52: Protein | Mass: 17574.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FJL7 |
#53: Protein | Mass: 16056.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7FTS1 |
#55: Protein | Mass: 7551.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4B4Z0 |
#56: Protein | Mass: 6455.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7ITW7 |
#58: Protein | Mass: 11995.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7F3F2 |
#62: Protein | Mass: 32216.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7H1U4 |
#63: Protein | Mass: 29741.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7I881 |
#64: Protein | Mass: 29959.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GQU3 |
#65: Protein | Mass: 22088.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7H0E8 |
#66: Protein | Mass: 24918.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HJ03 |
#68: Protein | Mass: 16265.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: P49215 |
#69: Protein | Mass: 9163.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7G7P4 |
#71: Protein | Mass: 14608.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7GRY8 |
#73: Protein | Mass: 28384.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7HSH1 |
#77: Protein | Mass: 15445.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A3Q7I5D6 |
#78: Protein | Mass: 9620.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A1U8DQX3 |
#79: Protein | Mass: 6953.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A0V0GRY5 |
#80: Protein | Mass: 14551.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: A0A1U7YEG5 |
-40S body ribosomal protein ... , 2 types, 2 molecules CAGA
#70: Protein | Mass: 15771.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4D3L7 |
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#74: Protein | Mass: 23051.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: K4ATQ2 |
-Sugars , 1 types, 1 molecules
#87: Sugar | ChemComp-BGC / |
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-Non-polymers , 7 types, 5222 molecules
#81: Chemical | ChemComp-K / #82: Chemical | ChemComp-MG / #83: Chemical | ChemComp-ZN / #84: Chemical | #85: Chemical | ChemComp-SPD / | #86: Chemical | ChemComp-PUT / | #88: 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: 80S ribosome / Type: RIBOSOME / Entity ID: #1-#80 / 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
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
3D reconstruction | Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335806 / Symmetry type: POINT |