- EMDB-8506: Structural Basis of Co-translational Quality Control by ArfA and ... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-8506
Title
Structural Basis of Co-translational Quality Control by ArfA and RF2 Binding to Ribosome
Map data
Sample
Complex: Non-stop ribosomal complex with ArfA and RF2
Complex: 30S subunit
Organelle or cellular component: 16S rRNA
RNA: 16S rRNA
Organelle or cellular component: 30S ribosomal protein S3
Protein or peptide: 30S ribosomal protein S3
Organelle or cellular component: 30S ribosomal protein S4
Protein or peptide: 30S ribosomal protein S4
Organelle or cellular component: 30S ribosomal protein S5
Organelle or cellular component: 30S ribosomal protein S12
Protein or peptide: 30S ribosomal protein S5
Protein or peptide: 30S ribosomal protein S12
Complex: 50S subunit
Organelle or cellular component: 23S rRNA
RNA: 23S rRNA
Organelle or cellular component: Alternative ribosome-rescue factor A
Protein or peptide: Alternative ribosome-rescue factor A
Organelle or cellular component: Peptide chain release factor 2
Protein or peptide: Peptide chain release factor 2
Organelle or cellular component: P-site tRNA fMet
RNA: P-site tRNA fMet
Organelle or cellular component: mRNA
RNA: mRNA
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 / rescue of stalled ribosome / mRNA regulatory element binding translation repressor activity / 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 / rescue of stalled ribosome / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / 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 S3, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S12, bacterial-type / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / K homology domain superfamily, prokaryotic type / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold Similarity search - Domain/homology
Peptide chain release factor RF2 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Alternative ribosome-rescue factor A Similarity search - Component
Biological species
Escherichia coli (E. coli)
Method
single particle reconstruction / cryo EM / Resolution: 3.7 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
-
Header (metadata) release
Jan 4, 2017
-
Map release
Jan 11, 2017
-
Update
Mar 13, 2024
-
Current status
Mar 13, 2024
Processing site: RCSB / Status: Released
-
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 / Details: Grids were blotted for 3.5 s.
-
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
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi