- EMDB-3581: Structure of 70S ribosome from Lactococcus lactis -
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Basic information
Entry
Database: EMDB / ID: EMD-3581
Title
Structure of 70S ribosome from Lactococcus lactis
Map data
Sample
Complex: 70S ribosome
RNA: x 3 types
Protein or peptide: x 48 types
Keywords
ribosome / 70S / lactoccocus lactis / Cryo-EM
Function / homology
Function and homology information
primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / zinc ion binding / cytoplasm Similarity search - Function
Ribosome hibernation promoting factor, long/plastid / 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 / Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S21, conserved site ...Ribosome hibernation promoting factor, long/plastid / 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 / Ribosomal protein L31 type B / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein S14/S29 / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / 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 S13, bacterial-type / 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 L34, conserved site / Ribosomal protein L34 signature. / 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 L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal L32p protein family Similarity search - Domain/homology
50S ribosomal protein L32 / 50S ribosomal protein L34 / 50S ribosomal protein L28 / 30S ribosomal protein S21 / 30S ribosomal protein S4 / Ribosome hibernation promotion factor / 50S ribosomal protein L31 type B / 30S ribosomal protein S16 / 50S ribosomal protein L27 / 50S ribosomal protein L21 ...50S ribosomal protein L32 / 50S ribosomal protein L34 / 50S ribosomal protein L28 / 30S ribosomal protein S21 / 30S ribosomal protein S4 / Ribosome hibernation promotion factor / 50S ribosomal protein L31 type B / 30S ribosomal protein S16 / 50S ribosomal protein L27 / 50S ribosomal protein L21 / 50S ribosomal protein L19 / 30S ribosomal protein S20 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 30S ribosomal protein S15 / 50S ribosomal protein L17 / 30S ribosomal protein S11 / 30S ribosomal protein S13 / 50S ribosomal protein L36 / 50S ribosomal protein L15 / 50S ribosomal protein L30 / 30S ribosomal protein S5 / 50S ribosomal protein L18 / 50S ribosomal protein L6 / 30S ribosomal protein S8 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L5 / 50S ribosomal protein L24 / 50S ribosomal protein L14 / 30S ribosomal protein S17 / 50S ribosomal protein L29 / 50S ribosomal protein L16 / 30S ribosomal protein S3 / 50S ribosomal protein L22 / 30S ribosomal protein S19 / 50S ribosomal protein L2 / 50S ribosomal protein L23 / 50S ribosomal protein L4 / 50S ribosomal protein L3 / 30S ribosomal protein S10 / 50S ribosomal protein L33 3 / 30S ribosomal protein S2 / 30S ribosomal protein S18 / 30S ribosomal protein S6 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 30S ribosomal protein S7 / 30S ribosomal protein S12 Similarity search - Component
Journal: Nat Commun / Year: 2017 Title: A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy. Authors: Linda E Franken / Gert T Oostergetel / Tjaard Pijning / Pranav Puri / Valentina Arkhipova / Egbert J Boekema / Bert Poolman / Albert Guskov / Abstract: Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion ...Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S ribosomes from Lactococcus lactis and a dimerization mechanism involving a single protein: HPF. The N-terminal domain of HPF binds at the same site as HPF in Escherichia coli 100S ribosomes. Contrary to ribosome modulation factor, the C-terminal domain of HPF binds exactly at the dimer interface. Furthermore, ribosomes from Lactococcus lactis do not undergo conformational changes in the 30S head domains upon binding of HPF, and the Shine-Dalgarno sequence and mRNA entrance tunnel remain accessible. Ribosome activity is blocked by HPF due to the inhibition of mRNA recognition by the platform binding center. Phylogenetic analysis of HPF proteins suggests that HPF-mediated dimerization is a widespread mechanism of ribosome hibernation in bacteria.When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.
History
Deposition
Jan 26, 2017
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Header (metadata) release
Feb 15, 2017
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Map release
Oct 11, 2017
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Update
May 15, 2024
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Current status
May 15, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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