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Yorodumi- PDB-3iz4: Modified E. coli tmRNA in the resume state with the tRNA-like dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iz4 | ||||||
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Title | Modified E. coli tmRNA in the resume state with the tRNA-like domain in the ribosomal P site interacting with the SmpB | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / transfer-messenger RNA / trans-translation / RNA / molecular mimicry / pseudo-knots / tRNA-like domain / mRNA-like domain / MS2 / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.6 Å | ||||||
Authors | Hashem, Y. / Fu, J. / Frank, J. | ||||||
Citation | Journal: EMBO J / Year: 2010 Title: Visualizing the transfer-messenger RNA as the ribosome resumes translation. Authors: Jie Fu / Yaser Hashem / Iwona Wower / Jianlin Lei / Hstau Y Liao / Christian Zwieb / Jacek Wower / Joachim Frank / Abstract: Bacterial ribosomes stalled by truncated mRNAs are rescued by transfer-messenger RNA (tmRNA), a dual-function molecule that contains a tRNA-like domain (TLD) and an internal open reading frame (ORF). ...Bacterial ribosomes stalled by truncated mRNAs are rescued by transfer-messenger RNA (tmRNA), a dual-function molecule that contains a tRNA-like domain (TLD) and an internal open reading frame (ORF). Occupying the empty A site with its TLD, the tmRNA enters the ribosome with the help of elongation factor Tu and a protein factor called small protein B (SmpB), and switches the translation to its own ORF. In this study, using cryo-electron microscopy, we obtained the first structure of an in vivo-formed complex containing ribosome and the tmRNA at the point where the TLD is accommodated into the ribosomal P site. We show that tmRNA maintains a stable 'arc and fork' structure on the ribosome when its TLD moves to the ribosomal P site and translation resumes on its ORF. Based on the density map, we built an atomic model, which suggests that SmpB interacts with the five nucleotides immediately upstream of the resume codon, thereby determining the correct selection of the reading frame on the ORF of tmRNA. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3iz4.cif.gz | 209.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iz4.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 3iz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iz4_validation.pdf.gz | 746.2 KB | Display | wwPDB validaton report |
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Full document | 3iz4_full_validation.pdf.gz | 784.7 KB | Display | |
Data in XML | 3iz4_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 3iz4_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/3iz4 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/3iz4 | HTTPS FTP |
-Related structure data
Related structure data | 5234MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: RNA chain | Mass: 121695.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MS2-tmRNA (H8), a variant of E. coli tmRNAH8 that can bind the coat protein from MS2 bacteriophage, was constructed by PCR-directed mutagenesis. Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 14046.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RR57 |
Sequence details | THE MODEL IS BASED ON THE CRYO-EM MAP OBTAINED FROM E. COLI. THE CHAIN B OF THE MODEL CONTAINS THE ...THE MODEL IS BASED ON THE CRYO-EM MAP OBTAINED FROM E. COLI. THE CHAIN B OF THE MODEL CONTAINS THE SEQUENCE FROM T. THERMOPHIL |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Modified transfer-messenger RNA bound to the ribosomal P site Type: RIBOSOME |
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Buffer solution | Name: Polymix buffer / pH: 7.5 / Details: Polymix buffer |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: Vitrification done with vitrobot plunging into liquid ethane. |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 100000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm |
Specimen holder | Specimen holder model: OTHER / Specimen holder type: CARTRIDGE |
Image recording | Electron dose: 24 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Volume | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: reference-based projection / Resolution: 13.6 Å / Num. of particles: 20873 / Nominal pixel size: 3 Å / Actual pixel size: 3 Å / Magnification calibration: 100000 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: METHOD--molecular dynamic flexible fitting REFINEMENT PROTOCOL--molecular dynamic flexible fitting | ||||||||||||
Refinement step | Cycle: LAST
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