- EMDB-3941: Structure of the chloroplast ribosome with chl-RRF and hibernatio... -
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Basic information
Entry
Database: EMDB / ID: EMD-3941
Title
Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor
Map data
Sample
Complex: Chloroplast ribosome in complex with RRF
RNA: x 4 types
Protein or peptide: x 53 types
Ligand: x 2 types
Function / homology
Function and homology information
plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / mitochondrial large ribosomal subunit / chloroplast envelope / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / mitochondrial translation / ribosomal small subunit binding ...plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / mitochondrial large ribosomal subunit / chloroplast envelope / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / mitochondrial translation / 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
30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosome hibernation promoting factor, long/plastid / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily ...30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosomal protein L6, chloroplast / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L32p, plant/cyanobacteria type / Ribosome hibernation promoting factor, long/plastid / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 30S ribosomal protein / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S3, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S19, bacterial-type / Ribosomal protein L20 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / : / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein S15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 Similarity search - Domain/homology
Large ribosomal subunit protein uL4c / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c / Large ribosomal subunit protein uL2cz/uL2cy / Small ribosomal subunit protein uS2c / Large ribosomal subunit protein uL22c / Small ribosomal subunit protein uS3c / Large ribosomal subunit protein uL14c / Small ribosomal subunit protein uS8c ...Large ribosomal subunit protein uL4c / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c / Large ribosomal subunit protein uL2cz/uL2cy / Small ribosomal subunit protein uS2c / Large ribosomal subunit protein uL22c / Small ribosomal subunit protein uS3c / Large ribosomal subunit protein uL14c / Small ribosomal subunit protein uS8c / Large ribosomal subunit protein bL36c / Large ribosomal subunit protein uL13c / Small ribosomal subunit protein uS4c / Large ribosomal subunit protein uL16c / Ribosome-binding factor PSRP1, chloroplastic / Large ribosomal subunit protein uL15c / Large ribosomal subunit protein bL35c / Large ribosomal subunit protein bL21c / Large ribosomal subunit protein uL24c / Large ribosomal subunit protein cL37 alpha / Large ribosomal subunit protein bL20c / Large ribosomal subunit protein bL32c / Large ribosomal subunit protein bL33c / Small ribosomal subunit protein bS16c / Small ribosomal subunit protein bTHXc / Small ribosomal subunit protein uS12cz/uS12cy / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS7cz/uS7cy / 30S ribosomal protein S20, chloroplastic / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS13c / Large ribosomal subunit protein bL9c / Large ribosomal subunit protein bL27c / Large ribosomal subunit protein uL3c / Large ribosomal subunit protein uL5c / Large ribosomal subunit protein uL6c / Large ribosomal subunit protein bL17c / Large ribosomal subunit protein uL18c / Ribosome-recycling factor, chloroplastic / Large ribosomal subunit protein bL34c / Large ribosomal subunit protein bL28c / Large ribosomal subunit protein uL29c / Large ribosomal subunit protein bL31c / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein bS6c alpha / Large ribosomal subunit protein cL38 / Large ribosomal subunit protein bL19c / Large ribosomal subunit protein uL23c / Small ribosomal subunit protein uS15c / Small ribosomal subunit protein bS18c / Small ribosomal subunit protein uS5c Similarity search - Component
Biological species
Spinacia oleracea (spinach) / Spinach (spinach)
Method
single particle reconstruction / cryo EM / Resolution: 3.0 Å
Journal: Nat Plants / Year: 2018 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
Deposition
Oct 18, 2017
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Header (metadata) release
Apr 18, 2018
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Map release
Apr 18, 2018
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Update
Nov 25, 2020
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Current status
Nov 25, 2020
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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