- EMDB-8505: Structural Basis of Co-translational Quality Control by ArfA and ... -
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Basic information
Entry
Database: EMDB / ID: EMD-8505
Title
Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome
Map data
Sample
Complex: Non-stop ribosomal complex with ArfA and RF2
Complex: 30S subunit
Complex: 30S ribosomal protein S2
Protein or peptide: x 1 types
Organelle or cellular component: 16S rRNA
RNA: x 1 types
Organelle or cellular component: 30S ribosomal protein S3
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S4
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S5
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S6
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S7
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S8
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S9
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S10
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S11
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S12
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S13
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S14
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S15
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S16
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S17
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S18
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S19
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S20
Protein or peptide: x 1 types
Organelle or cellular component: 30S ribosomal protein S21
Protein or peptide: x 1 types
Complex: 50S subunit
Complex: 50S ribosomal protein L25
Protein or peptide: x 1 types
Organelle or cellular component: 23S rRNA
RNA: x 1 types
Organelle or cellular component: 50S ribosomal protein L2
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L3
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L4
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L5
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L6
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L9
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L11
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L13
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L14
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L15
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L16
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L17
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L18
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L19
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L20
Organelle or cellular component: 50S ribosomal protein L21
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L22
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L23
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L24
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L27
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L28
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L29
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L30
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L32
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L33
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L34
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L35
Protein or peptide: x 1 types
Organelle or cellular component: 50S ribosomal protein L36
Protein or peptide: x 1 types
Organelle or cellular component: 5S rRNA
RNA: x 1 types
Protein or peptide: x 1 types
Organelle or cellular component: Alternative ribosome-rescue factor A
Protein or peptide: x 1 types
Organelle or cellular component: Peptide chain release factor 2
Protein or peptide: x 1 types
Organelle or cellular component: P-site or E-site fMet-tRNA(fMet)
RNA: x 1 types
Organelle or cellular component: mRNA
RNA: x 1 types
Ligand: x 2 types
Function / homology
Function and homology information
translation release factor activity, codon specific / stringent response / mRNA base-pairing translational repressor activity / ribosomal large subunit binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation ...translation release factor activity, codon specific / stringent response / mRNA base-pairing translational repressor activity / ribosomal large subunit binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / rescue of stalled ribosome / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / 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 / tRNA binding / cytoplasmic translation / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function
Alternative ribosome-rescue factor A / Alternative ribosome-rescue factor A / Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain ...Alternative ribosome-rescue factor A / Alternative ribosome-rescue factor A / Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / 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 L17 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / 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 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 L9/RNase H1, N-terminal / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / 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 Similarity search - Domain/homology
Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Peptide chain release factor RF2 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 ...Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Peptide chain release factor RF2 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Alternative ribosome-rescue factor A / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 Similarity search - Component
Biological species
Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Method
single particle reconstruction / cryo EM / Resolution: 3.5 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01GM120552
United States
Citation
Journal: Nature / Year: 2017 Title: Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. Authors: Fuxing Zeng / Yanbo Chen / Jonathan Remis / Mrinal Shekhar / James C Phillips / Emad Tajkhorshid / Hong Jin / Abstract: Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs ...Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome.
History
Deposition
Dec 4, 2016
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Header (metadata) release
Jan 4, 2017
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Map release
Jan 11, 2017
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Update
Dec 2, 2020
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Current status
Dec 2, 2020
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
JEOL 3200FSC
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 4-25 / Average exposure time: 6.0 sec. / Average electron dose: 20.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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