- PDB-5h1s: Structure of the large subunit of the chloro-ribosome -
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Basic information
Entry
Database: PDB / ID: 5h1s
Title
Structure of the large subunit of the chloro-ribosome
Components
(50S ribosomal protein ...) x 29
23S rRNA23S ribosomal RNA
5S rRNA5S ribosomal RNA
Spinach chloroplast 4.5S rRNA
Keywords
RIBOSOME / Cryo-EM / chloro-ribosome
Function / homology
Function and homology information
plastid translation / mitochondrial translation / mitochondrial large ribosomal subunit / chloroplast / ribosome assembly / DNA-templated transcription, termination / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit ...plastid translation / mitochondrial translation / mitochondrial large ribosomal subunit / chloroplast / ribosome assembly / DNA-templated transcription, termination / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / transferase activity / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / mitochondrion / RNA binding Similarity search - Function
Ribosomal protein L28/L24 / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L6, chloroplast / Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; ...Ribosomal protein L28/L24 / 50S ribosomal protein 5, chloroplastic / Family of unknown function (DUF5323) / Ribosomal protein L6, chloroplast / Ribosomal protein L32p, plant/cyanobacteria type / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal Protein L24e; Chain: T; / Ribosomal protein L6 / Ribosomal protein L5 / 50s Ribosomal Protein L5; Chain: A, / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal Protein L22; Chain A / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / RRM (RNA recognition motif) domain / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / 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 signature 2. / Ribosomal protein L16, conserved site / 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 L28/L24 superfamily / Single Sheet / Ribosomal protein L36 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L9 / Ribosomal protein L35, conserved site / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35 signature. / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9, N-terminal / Nucleic acid-binding proteins / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L20 signature. / Ribosomal protein L27 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal L28 family / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L18 / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L20 / Ribosomal protein L34 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L34 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / Ribosomal prokaryotic L21 protein / L21-like superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L13, bacterial-type / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type Similarity search - Domain/homology
RNA (> 1000) / 50S ribosomal protein L3, chloroplastic / 50S ribosomal protein L21, chloroplastic / 50S ribosomal protein L24, chloroplastic / 50S ribosomal protein 5 alpha, chloroplastic / 50S ribosomal protein L20, chloroplastic / 50S ribosomal protein L32, chloroplastic / 50S ribosomal protein L33, chloroplastic / 50S ribosomal protein L9, chloroplastic / 50S ribosomal protein L27, chloroplastic ...RNA (> 1000) / 50S ribosomal protein L3, chloroplastic / 50S ribosomal protein L21, chloroplastic / 50S ribosomal protein L24, chloroplastic / 50S ribosomal protein 5 alpha, chloroplastic / 50S ribosomal protein L20, chloroplastic / 50S ribosomal protein L32, chloroplastic / 50S ribosomal protein L33, chloroplastic / 50S ribosomal protein L9, chloroplastic / 50S ribosomal protein L27, chloroplastic / 50S ribosomal protein L6, chloroplastic / 50S ribosomal protein L5, chloroplastic / 50S ribosomal protein L15, chloroplastic / 50S ribosomal protein L17, chloroplastic / 50S ribosomal protein L18, chloroplastic / 50S ribosomal protein L34, chloroplastic / 50S ribosomal protein L28, chloroplastic / 50S ribosomal protein L29, chloroplastic / 50S ribosomal protein L31, chloroplastic / 50S ribosomal protein 6, chloroplastic / 50S ribosomal protein L19, chloroplastic / 50S ribosomal protein L35, chloroplastic / 50S ribosomal protein L16, chloroplastic / RNA (> 100) / 50S ribosomal protein L27, chloroplastic / RNA (> 10) / RNA / : / : / 50S ribosomal protein L3, chloroplastic / 50S ribosomal protein L15, chloroplastic / 50S ribosomal protein L18, chloroplastic / 50S ribosomal protein L31, chloroplastic / 50S ribosomal protein L6, chloroplastic / 50S ribosomal protein L13, chloroplastic / 50S ribosomal protein L29, chloroplastic / 50S ribosomal protein L28, chloroplastic / 50S ribosomal protein L17, chloroplastic / 50S ribosomal protein L9, chloroplastic / 50S ribosomal protein L4, chloroplastic / 50S ribosomal protein L2, chloroplastic / 50S ribosomal protein L22, chloroplastic / 50S ribosomal protein L14, chloroplastic / 50S ribosomal protein L36, chloroplastic / 50S ribosomal protein L23, chloroplastic Similarity search - Component
Biological species
Spinacia oleracea (spinach)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
Journal: Sci Rep / Year: 2016 Title: Cryo-EM structure of the large subunit of the spinach chloroplast ribosome. Authors: Tofayel Ahmed / Zhan Yin / Shashi Bhushan / Abstract: Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ...Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 Å. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features.
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
Electron dose: 26 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1590
Image scans
Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7
Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174949 / Algorithm: FOURIER SPACE / Num. of class averages: 20 / Symmetry type: POINT
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
ELECTRONMICROSCOPY
f_bond_d
0.013
98895
ELECTRONMICROSCOPY
f_angle_d
1.234
148525
ELECTRONMICROSCOPY
f_dihedral_angle_d
20.893
58950
ELECTRONMICROSCOPY
f_chiral_restr
0.06
18988
ELECTRONMICROSCOPY
f_plane_restr
0.053
8212
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