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Yorodumi- PDB-5u4j: Structural Basis of Co-translational Quality Control by ArfA and ... -
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-Basic information
Entry | Database: PDB / ID: 5u4j | ||||||
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Title | Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome | ||||||
Components |
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Keywords | RIBOSOME / ArfA / RF2 / nonstop translation | ||||||
Function / homology | Function and homology information translation release factor activity, codon specific / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / rescue of stalled ribosome / positive regulation of RNA splicing ...translation release factor activity, codon specific / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / rescue of stalled ribosome / positive regulation of RNA splicing / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / viral translational frameshifting / translation / response to antibiotic / mRNA binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Zeng, F. / Chen, Y. / Remis, J. / Shekhar, M. / Phillips, J.C. / Tajkhorshid, E. / Jin, H. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 5u4j.cif.gz | 401.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u4j.ent.gz | 250.9 KB | Display | PDB format |
PDBx/mmJSON format | 5u4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u4j_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5u4j_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5u4j_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 5u4j_validation.cif.gz | 63.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/5u4j ftp://data.pdbj.org/pub/pdb/validation_reports/u4/5u4j | HTTPS FTP |
-Related structure data
Related structure data | 8506MC 8505C 5u4iC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
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-Components
-RNA chain , 4 types, 4 molecules aAzx
#1: RNA chain | Mass: 497075.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 817573384 |
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#2: RNA chain | Mass: 941790.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 42756 |
#6: RNA chain | Mass: 5922.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
#7: RNA chain | Mass: 24786.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA was prepared by in vitro transcription / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 687670942 |
-30S ribosomal protein ... , 4 types, 4 molecules cdel
#3: Protein | Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsC b3314 JW3276 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V3 |
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#4: Protein | Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsD ramA b3296 JW3258 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V8 |
#5: Protein | Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsE spc b3303 JW3265 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W1 |
#8: Protein | Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene Name(s): rpsL strA b3342 JW3304 / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7S3 |
-Protein , 2 types, 2 molecules vw
#9: Protein | Mass: 43299.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Gene Name(s): prfB ECK2886 JW5847 supK / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: prfB, supK, b2891, JW5847 / Production host: Escherichia coli (E. coli) / References: UniProt: P07012 |
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#10: Protein | Mass: 6513.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Gene Name(s): arfA ECK3278 JW3253 yhdL / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: arfA, yhdL, b4550, JW3253 / Production host: Escherichia coli (E. coli) / References: UniProt: P36675 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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