[English] 日本語
Yorodumi- PDB-6dnc: E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dnc | ||||||
---|---|---|---|---|---|---|---|
Title | E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codon | ||||||
Components |
| ||||||
Keywords | RIBOSOME / RF1 / sense codon / cryo-EM | ||||||
Function / homology | Function and homology information translation release factor activity, codon specific / ribosomal large subunit assembly / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit ...translation release factor activity, codon specific / ribosomal large subunit assembly / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / 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 / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / RNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Svidritskiy, E. / Demo, G. / Korostelev, A.A. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J Biol Chem / Year: 2018 Title: Mechanism of premature translation termination on a sense codon. Authors: Egor Svidritskiy / Gabriel Demo / Andrei A Korostelev / Abstract: Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose ...Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose accumulation could be detrimental to the cell. Nevertheless, some sense codons are prone to triggering premature termination, but the structural basis for this is unclear. To investigate premature termination, we determined a cryo-EM structure of the 70S ribosome bound with RF1 in response to a UAU (Tyr) sense codon. The structure reveals that RF1 recognizes a UAU codon similarly to a UAG stop codon, suggesting that sense codons induce premature termination because they structurally mimic a stop codon. Hydrophobic interaction between the nucleobase of U3 (the third position of the UAU codon) and conserved Ile-196 in RF1 is important for misreading the UAU codon. Analyses of RNA binding in ribonucleoprotein complexes or by amino acids reveal that Ile-U packing is a frequent protein-RNA-binding motif with key functional implications. We discuss parallels with eukaryotic translation termination by the release factor eRF1. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6dnc.cif.gz | 3.8 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dnc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6dnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dnc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6dnc_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6dnc_validation.xml.gz | 241.2 KB | Display | |
Data in CIF | 6dnc_validation.cif.gz | 407.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/6dnc ftp://data.pdbj.org/pub/pdb/validation_reports/dn/6dnc | HTTPS FTP |
-Related structure data
Related structure data | 7970MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 5 types, 6 molecules ABCDLAKA
#1: RNA chain | Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1338015391 | ||
---|---|---|---|
#2: RNA chain | Mass: 941321.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1036415628 | ||
#3: RNA chain | Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1370526515 | ||
#4: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: GenBank: 1384458579 #37: RNA chain | | Mass: 8839.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
+50S ribosomal protein ... , 32 types, 32 molecules EFGHIJKLMNOPQRSTUVWXYZAABACADAEAFAGAHAIAJA
-Protein , 1 types, 1 molecules MA
#38: Protein | Mass: 40815.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prfA, ECS88_1279 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: B7MKB3 |
---|
-30S ribosomal protein ... , 20 types, 20 molecules OAPAQARASATAUAVAWAXAYAZAABBBCBDBEBFBGBHB
#39: Protein | Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MBF0 |
---|---|
#40: Protein | Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS9 |
#41: Protein | Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCR2 |
#42: Protein | Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7W1 |
#43: Protein | Mass: 15211.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P02358 |
#44: Protein | Mass: 17637.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCV6 |
#45: Protein | Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS1 |
#46: Protein | Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MBZ1 |
#47: Protein | Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCT6 |
#48: Protein | Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCR3 |
#49: Protein | Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCV7 |
#50: Protein | Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P0A7S9 |
#51: Protein | Mass: 11677.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS2 |
#52: Protein | Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MB86 |
#53: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MIU7 |
#54: Protein | Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCS6 |
#55: Protein | Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MLK7 |
#56: Protein | Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MCT1 |
#57: Protein | Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: B7MAE3 |
#58: Protein | Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600 / References: UniProt: P68679 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 2.5 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 7 Details: 20 mM Tris-HCl, 100 mM NH4Cl, 20.5 mM MgCl2, 0.5 mM EDTA, 6 mM beta-mercaptoethanol | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: PELCO easiGlow glow discharge unit, negative 20 mA. Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 0.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3963 |
Image scans | Movie frames/image: 80 / Used frames/image: 3-42 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1065147 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 639088 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 200 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient |