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- PDB-6eri: Structure of the chloroplast ribosome with chl-RRF and hibernatio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6eri | |||||||||||||||
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Title | Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor | |||||||||||||||
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![]() | RIBOSOME / Chloroplast / translation | |||||||||||||||
Function / homology | ![]() plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / mitochondrial translation / chloroplast thylakoid membrane ...plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / chloroplast envelope / mitochondrial large ribosomal subunit / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / mitochondrial translation / chloroplast thylakoid membrane / ribosomal small subunit binding / 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 / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||||||||
![]() | Perez Borema, A. / Aibara, S. / Paul, B. / Tobiasson, V. / Kimanius, D. / Forsberg, B.O. / Wallden, K. / Lindahl, E. / Amunts, A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor. Authors: Annemarie Perez Boerema / Shintaro Aibara / Bijoya Paul / Victor Tobiasson / Dari Kimanius / Björn O Forsberg / Karin Wallden / Erik Lindahl / A Amunts / ![]() ![]() Abstract: Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions ...Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome. Despite recent structural information, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9-3.1 Å resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes. | |||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 3.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3941MC ![]() 3942C ![]() 3943C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 4 types, 4 molecules AAABAxBA
#1: RNA chain | Mass: 911344.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 34334.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#32: RNA chain | Mass: 38072.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#34: RNA chain | Mass: 480386.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+50S ribosomal protein ... , 29 types, 29 molecules ACADAEAFAGAHAJAKALAMANAOAPAQARASATAUAWAXAYAZAaAbAcAdAeAfAw
-Protein , 3 types, 3 molecules AzBVBY
#33: Protein | Mass: 21643.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#55: Protein | Mass: 11938.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#57: Protein | Mass: 14485.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+30S ribosomal protein ... , 21 types, 21 molecules BBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBW
-Non-polymers , 2 types, 345 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#58: Chemical | ChemComp-MG / #59: Chemical | |
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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 | Name: Chloroplast ribosome in complex with RRF / Type: RIBOSOME / Entity ID: #1-#57 / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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 |
Image recording | Electron dose: 4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130300 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |