- EMDB-24307: Structure of the translating Neurospora crassa ribosome arrested ... -
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Basic information
Entry
Database: EMDB / ID: EMD-24307
Title
Structure of the translating Neurospora crassa ribosome arrested by cycloheximide
Map data
Sample
Complex: Structure of the translating Neurospora crassa ribosome arrested by cycloheximide
Complex: 60S ribosomal subunit
RNA: x 3 types
Protein or peptide: x 42 types
Complex: 40S ribosomal subunit
RNA: x 1 types
Protein or peptide: x 33 types
Complex: tRNA
RNA: x 1 types
Complex: Nascent peptide
Protein or peptide: x 1 types
Complex: mRNA
RNA: x 1 types
Ligand: x 3 types
Keywords
Protein Synthesis Inhibitor / Cytosolic Ribosome / Polysomal Ribosome / Peptidyl Transferase Center / TRANSLATION
Function / homology
Function and homology information
: / positive regulation of translational fidelity / preribosome, small subunit precursor / protein kinase A catalytic subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / ribosomal small subunit export from nucleus / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity ...: / positive regulation of translational fidelity / preribosome, small subunit precursor / protein kinase A catalytic subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / ribosomal small subunit export from nucleus / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / ribosomal large subunit assembly / modification-dependent protein catabolic process / rRNA processing / large ribosomal subunit / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function
Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e ...Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L19/L19e conserved site / Ribosomal protein L44 / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L23/L25, N-terminal Similarity search - Domain/homology
Uncharacterized protein / 60S ribosomal protein L35 / 40S ribosomal protein S7 / 60S ribosomal protein L5 / 40S ribosomal protein S21 / 60S ribosomal protein L28 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S26E / 40S ribosomal protein S17 / 60S ribosomal protein L3 ...Uncharacterized protein / 60S ribosomal protein L35 / 40S ribosomal protein S7 / 60S ribosomal protein L5 / 40S ribosomal protein S21 / 60S ribosomal protein L28 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S26E / 40S ribosomal protein S17 / 60S ribosomal protein L3 / 40S ribosomal protein S0 / Guanine nucleotide-binding protein subunit beta-like protein / Ribosomal protein L26 / 60S ribosomal protein L27 / 40S ribosomal protein S24 / 60S ribosomal protein L22 / 60S ribosomal protein L4-A / 60S ribosomal protein L8 / Cytoplasmic ribosomal protein 10 / 40S ribosomal protein S12 / 40S ribosomal protein S22 / 40S ribosomal protein S5 / 60S ribosomal protein L44 / 60S ribosomal protein L11 / 40S ribosomal protein S27 / 60S ribosomal protein L2 / 60S ribosomal protein L34 / 60s ribosomal protein / 60S ribosomal protein L18 / 40S ribosomal protein S18 / 60S ribosomal protein L32 / 60S ribosomal protein L29 / 60S ribosomal protein L33 / 60S ribosomal protein L43 / 60S ribosomal protein L39 / 40S ribosomal protein S20 / 40S ribosomal protein S2 / Ribosomal protein L19 / 40S ribosomal protein S28 / 60S ribosomal protein L13 / 60S ribosomal protein L10 / 60S ribosomal protein L30 / Ribosomal_L28e domain-containing protein / 60S ribosomal protein L7 / 40S ribosomal protein S19 / 60S ribosomal protein L25 / 40S ribosomal protein S25 / 40S ribosomal protein S13 / 60S ribosomal protein L24 / 40S ribosomal protein S9 / Ribosomal protein Srp1 / 40S ribosomal protein S4 / 60S ribosomal protein L36 / 40S ribosomal protein S16 / 40S ribosomal protein S11 / 60S ribosomal protein L9 / Ribosomal protein S12 / 60S ribosomal protein L6 / 60S ribosomal protein L23 / Ribosomal protein L14 / 40S ribosomal protein S1 / Probable 40s ribosomal protein s10-b / 60S ribosomal protein L15 / 60S ribosomal protein L38 / 40S ribosomal protein S29 / 60S ribosomal protein L17 / 40S ribosomal protein S23 / 60S ribosomal protein L41 / 60S ribosomal protein L16 / 40S ribosomal protein S30 / 60S ribosomal protein L40 / 40S ribosomal protein S6 / 40S ribosomal protein S8 / Ribosomal protein L37 / 60S ribosomal protein L20 Similarity search - Component
Biological species
Neurospora crassa (fungus)
Method
single particle reconstruction / cryo EM / Resolution: 2.7 Å
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
R21AI138158
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R35 GM126966
United States
Welch Foundation
A1863
United States
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structure of the translating ribosome arrested by cycloheximide. Authors: Lunda Shen / Zhaoming Su / Kailu Yang / Cheng Wu / Thomas Becker / Deborah Bell-Pedersen / Junjie Zhang / Matthew S Sachs / Abstract: Ribosomes translate RNA into proteins. The protein synthesis inhibitor cycloheximide (CHX) is widely used to inhibit eukaryotic ribosomes engaged in translation elongation. However, the lack of ...Ribosomes translate RNA into proteins. The protein synthesis inhibitor cycloheximide (CHX) is widely used to inhibit eukaryotic ribosomes engaged in translation elongation. However, the lack of structural data for actively translating polyribosomes stalled by CHX leaves unanswered the question of which elongation step is inhibited. We elucidated CHX's mechanism of action based on the cryo-electron microscopy structure of actively translating ribosomes bound with CHX at 2.7-Å resolution. The ribosome structure from this filamentous fungus contains clearly resolved ribosomal protein eL28, like higher eukaryotes but unlike budding yeast, which lacks eL28. Despite some differences in overall structures, the ribosomes from , yeast, and humans all contain a highly conserved CHX binding site. We also sequenced classic CHX-resistant alleles. These mutations, including one at a residue not previously observed to affect CHX resistance in eukaryotes, were in the large subunit proteins uL15 and eL42 that are part of the CHX-binding pocket. In addition to A-site transfer RNA (tRNA), P-site tRNA, messenger RNA, and CHX that are associated with the translating ribosome, spermidine is present near the CHX binding site close to the E site on the large subunit. The tRNAs in the peptidyl transferase center are in the A/A site and the P/P site. The nascent peptide is attached to the A-site tRNA and not to the P-site tRNA. The structural and functional data obtained show that CHX arrests the ribosome in the classical PRE translocation state and does not interfere with A-site reactivity.
History
Deposition
Jun 25, 2021
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Header (metadata) release
Dec 1, 2021
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Map release
Dec 1, 2021
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Update
Jun 5, 2024
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Current status
Jun 5, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Name: tRNA / type: rna / ID: 80 Details: One molecule is found in the A-site, and one molecule is found in the P-site. No specific tRNAs are represented in the peptidyltransferase centers of polysomal ribosomes. Therefore, we ...Details: One molecule is found in the A-site, and one molecule is found in the P-site. No specific tRNAs are represented in the peptidyltransferase centers of polysomal ribosomes. Therefore, we adapted the tRNA model for a eukaryotic ICG-anticodon tRNA that decodes Arg codons (PDB ID: 6T4Q) to model the tRNA densities of both A- and P-site tRNAs. Number of copies: 2
Name: mRNA / type: rna / ID: 82 Details: No specific mRNA is represented in the polysomal ribosomes. Therefore, we used Uracil to model the mRNA. Number of copies: 1
Source (natural)
Organism: Neurospora crassa (fungus)
Molecular weight
Theoretical: 5.159861 KDa
Sequence
String:
UUUUUUUUUU UUUUUUU
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Macromolecule #4: 40S ribosomal protein S0
Macromolecule
Name: 40S ribosomal protein S0 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
UniProtKB: Ribosomal_L28e domain-containing protein
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Macromolecule #81: Nascent peptide
Macromolecule
Name: Nascent peptide / type: protein_or_peptide / ID: 81 Details: No specific nascent peptide is represented in the polysomal ribosomes. Therefore, we used UNK (unknown residue) to represent each residue of the nascent peptide. Number of copies: 1 / Enantiomer: LEVO
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