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Open data
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Basic information
Entry | Database: PDB / ID: 5x8p | ||||||
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Title | Structure of the 70S chloroplast ribosome from spinach | ||||||
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![]() | RIBOSOME / Cryo-EM / chloroplast ribosome | ||||||
Function / homology | ![]() plastid small ribosomal subunit / plastid translation / chloroplast rRNA processing / negative regulation of translational elongation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / plastid / mitochondrial translation / chloroplast stroma ...plastid small ribosomal subunit / plastid translation / chloroplast rRNA processing / negative regulation of translational elongation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / plastid / mitochondrial translation / chloroplast stroma / ribosomal small subunit binding / chloroplast thylakoid membrane / chloroplast / DNA-templated transcription termination / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / mitochondrion / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | Ahmed, T. / Shi, J. / Bhushan, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation. Authors: Tofayel Ahmed / Jian Shi / Shashi Bhushan / ![]() Abstract: Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, ...Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 221.4 KB | Display | |
Data in CIF | ![]() | 380.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6709MC ![]() 6710C ![]() 6711C ![]() 5x8rC ![]() 5x8tC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-50S ribosomal protein ... , 18 types, 18 molecules 12345CEFKLNQRSTUV0
#1: Protein | Mass: 6519.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 7536.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 6789.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 8459.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein/peptide | Mass: 4414.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 29722.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 27202.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 24248.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 22774.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#16: Protein | Mass: 13484.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#18: Protein | Mass: 15328.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#21: Protein | Mass: 17597.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#22: Protein | Mass: 15594.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#23: Protein | Mass: 22793.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#24: Protein | Mass: 23292.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 13575.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 16552.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#32: Protein | Mass: 10801.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 18 types, 18 molecules 67DGHMOPXYZjqtuywv
#6: Protein | Mass: 15694.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#7: Protein | Mass: 12080.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 24117.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 20263.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 17669.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein | Mass: 20680.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#19: Protein | Mass: 13466.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#20: Protein | Mass: 13801.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 15326.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#29: Protein | Mass: 9016.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#30: Protein | Mass: 12903.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#40: Protein | Mass: 13882.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#46: Protein | Mass: 12195.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 12178.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#50: Protein | Mass: 16096.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#51: Protein | Mass: 26851.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#53: Protein | Mass: 13808.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#55: Protein | Mass: 21691.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 4 types, 4 molecules BWAa
#8: RNA chain | Mass: 39014.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#27: RNA chain | Mass: 34334.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#31: RNA chain | Mass: 911344.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#52: RNA chain | Mass: 483466.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-30S ribosomal protein ... , 17 types, 17 molecules bcefghiklmoprsdn8
#33: Protein | Mass: 26736.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#34: Protein | Mass: 24965.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#35: Protein | Mass: 27696.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#36: Protein | Mass: 16341.423 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#37: Protein | Mass: 17378.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#38: Protein | Mass: 15527.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#39: Protein | Mass: 17092.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#41: Protein | Mass: 14927.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein | Mass: 13794.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#43: Protein | Mass: 14418.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#44: Protein | Mass: 10778.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#45: Protein | Mass: 10454.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#47: Protein | Mass: 12079.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#48: Protein | Mass: 10632.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#54: Protein | Mass: 23454.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#56: Protein | Mass: 11809.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#58: Protein | Mass: 40472.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 1 types, 1 molecules x
#57: Protein/peptide | Mass: 5188.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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 |
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Sample preparation
Component |
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Molecular weight | Value: 1.7 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Buffer solution | pH: 7.6 Details: 20 mM Tris HCl, pH 7.6, 100 mM KCl, 10 mM MgOAc, 100 mM sucrose, 7 mM 2-mercaptoethanol, 1 unit/ml RNase inhibitor, 0.1% protease inhibitor | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 133333 X / Nominal defocus max: 3700 nm / Nominal defocus min: 400 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3700 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3161 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 25 / Used frames/image: 1-25 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||||||||
Particle selection | Num. of particles selected: 187946 | |||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81305 / Algorithm: FOURIER SPACE / Symmetry type: POINT |