+Open data
-Basic information
Entry | Database: PDB / ID: 5mmi | ||||||
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Title | Structure of the large subunit of the chloroplast ribosome | ||||||
Components |
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Keywords | RIBOSOME / chloroplast / translation / cryo-EM | ||||||
Function / homology | Function and homology information plastid translation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding ...plastid translation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial translation / chloroplast / DNA-templated transcription termination / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / mitochondrion / RNA binding Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Bieri, P. / Leibundgut, M. / Saurer, M. / Boehringer, D. / Ban, N. | ||||||
Citation | Journal: EMBO J / Year: 2017 Title: The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. Authors: Philipp Bieri / Marc Leibundgut / Martin Saurer / Daniel Boehringer / Nenad Ban / Abstract: Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, ...Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5mmi.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5mmi.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 5mmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mmi_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5mmi_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5mmi_validation.xml.gz | 168.2 KB | Display | |
Data in CIF | 5mmi_validation.cif.gz | 281 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/5mmi ftp://data.pdbj.org/pub/pdb/validation_reports/mm/5mmi | HTTPS FTP |
-Related structure data
Related structure data | 3531MC 3532C 3533C 5mmjC 5mmmC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-50S ribosomal protein ... , 17 types, 17 molecules 0123457CJKLNQRSTU
#1: Protein | Mass: 14748.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R0R6, UniProt: P82249*PLUS |
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#2: Protein | Mass: 6650.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28804 |
#3: Protein | Mass: 7668.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Zn-binding protein / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28805 |
#4: Protein | Mass: 16126.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82244 |
#5: Protein | Mass: 17376.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P23326 |
#6: Protein/peptide | Mass: 4414.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Zn-binding protein / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12230 |
#8: Protein | Mass: 12080.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82411 |
#11: Protein | Mass: 29853.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06509 |
#18: Protein | Mass: 23689.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P31164 |
#19: Protein | Mass: 28211.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12629 |
#20: Protein | Mass: 13484.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09596 |
#22: Protein | Mass: 15328.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17353 |
#25: Protein | Mass: 26121.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82413 |
#26: Protein | Mass: 15725.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28803 |
#27: Protein | Mass: 28441.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Residues 68-81 were built as poly-alanine and deposited as UNK. Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P24613 |
#28: Protein | Mass: 23292.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09594 |
#29: Protein | Mass: 21832.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9LWB5 |
-Plastid ribosomal protein ... , 14 types, 14 molecules 6DEFGHIMOPVXYZ
#7: Protein | Mass: 15694.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9S2M7, UniProt: P27684*PLUS |
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#12: Protein | Mass: 33034.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QEC7, UniProt: P82191*PLUS |
#13: Protein | Mass: 32541.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RVQ9, UniProt: O49937*PLUS |
#14: Protein | Mass: 28182.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Residues 39-52 were built as poly-alanine and deposited as UNK. Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RJX4, UniProt: P82192*PLUS |
#15: Protein | Mass: 24516.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4N9, UniProt: P82193*PLUS |
#16: Protein | Mass: 22038.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RQ91, UniProt: P82180*PLUS |
#17: Protein | Mass: 26128.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R3N5, UniProt: P82139*PLUS |
#21: Protein | Mass: 29081.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHT0, UniProt: P22798*PLUS |
#23: Protein | Mass: 14577.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RLJ4, UniProt: P82194*PLUS |
#24: Protein | Mass: 18410.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QQ60, UniProt: P82195*PLUS |
#30: Protein | Mass: 21417.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QFU9, UniProt: P27683*PLUS |
#32: Protein | Mass: 21366.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R4I2, UniProt: P82190*PLUS |
#33: Protein | Mass: 16460.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RD02, UniProt: P82245*PLUS |
#34: Protein | Mass: 19083.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R7W8, UniProt: P82248*PLUS |
-RNA chain , 4 types, 4 molecules ABWz
#9: RNA chain | Mass: 911344.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084 |
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#10: RNA chain | Mass: 39014.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) |
#31: RNA chain | Mass: 34334.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 12299 |
#35: RNA chain | Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CA-3' end of E-site tRNA / Source: (natural) Spinacia oleracea (spinach) |
-Non-polymers , 2 types, 503 molecules
#36: Chemical | #37: Chemical | ChemComp-MG / |
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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: Chloroplast 70S ribosome / Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 2.4 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Spinacia oleracea (spinach) / Organelle: chloroplast / Tissue: leaf | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.6 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278 K |
-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 magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 2796 |
Image scans | Movie frames/image: 8 / Used frames/image: 2-8 |
-Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 326094 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154332 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 56.9 / Protocol: OTHER / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.2→3.2 Å / SU ML: 0.44 / σ(F): 1.06 / Phase error: 26.15 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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