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Yorodumi- PDB-1zc8: Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zc8 | ||||||
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Title | Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map of the 70S ribosome and tmRNA complex | ||||||
Components |
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Keywords | RNA binding protein/RNA / SmpB / tmRNA / EF-Tu / h44 / 30S / 16s rRNA / Cryo-EM / trans-translation / 70S / RNA binding protein-RNA COMPLEX | ||||||
Function / homology | Function and homology information trans-translation / translation elongation factor activity / GTPase activity / GTP binding / RNA binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13 Å | ||||||
Authors | Valle, M. / Gillet, R. / Kaur, S. / Henne, A. / Ramakrishnan, V. / Frank, J. | ||||||
Citation | Journal: Science / Year: 2003 Title: Visualizing tmRNA entry into a stalled ribosome. Authors: Mikel Valle / Reynald Gillet / Sukhjit Kaur / Anke Henne / V Ramakrishnan / Joachim Frank / Abstract: Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation ...Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation then switches from the defective message to a short open reading frame on tmRNA that tags the defective nascent peptide chain for degradation. However, the mechanism by which tmRNA can enter and move through the ribosome is unknown. We present a cryo-electron microscopy study at approximately 13 to 15 angstroms of the entry of tmRNA into the ribosome. The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA. #1: Journal: Embo J. / Year: 2002 Title: Structure of small protein B: the protein component of the tmRNA SmpB system for ribosome rescue Authors: Dong, G. / Nowakowski, J. / Hoffman, D.W. #2: Journal: Nucleic Acids Res. / Year: 2001 Title: tmRDB (tmRNA database) Authors: Knudsen, B. / Wower, J. / Zwieb, C. / Gorodkin, J. #3: Journal: Embo J. / Year: 2002 Title: Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process Authors: Valle, M. / Sengupta, J. / Swami, N.K. / Grassucci, R.A. / Burkhardt, N. / Nierhaus, K.H. / Agrawal, R.K. / Frank, J. #4: Journal: Structure Fold.Des. / Year: 1999 Title: E. Coli Cysteinyl-tRNA and T. Aquaticus Elongation Factor Ef-Tu: GTP Ternary Complex Authors: Nissen, P. / Kjeldgaard, M. / Thirup, S. / Nyborg, J. #5: Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form Authors: Ogle, J.M. / Murphy Iv, F.V. / Tarry, M.J. / Ramakrishnan, V. | ||||||
History |
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Remark 999 | SEQUENCE Author states that the map was for Thermus thermophilus, but the EF-Tu model was from ...SEQUENCE Author states that the map was for Thermus thermophilus, but the EF-Tu model was from Thermus aquaticus (SWS code Q01698). |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1zc8.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zc8.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 1zc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zc8_validation.pdf.gz | 829.5 KB | Display | wwPDB validaton report |
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Full document | 1zc8_full_validation.pdf.gz | 829 KB | Display | |
Data in XML | 1zc8_validation.xml.gz | 18 KB | Display | |
Data in CIF | 1zc8_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/1zc8 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/1zc8 | HTTPS FTP |
-Related structure data
Related structure data | 1122MC 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
-RNA chain , 5 types, 5 molecules ABCFZ
#1: RNA chain | Mass: 18951.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
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#2: RNA chain | Mass: 5162.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
#3: RNA chain | Mass: 10013.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
#5: RNA chain | Mass: 9206.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
#9: RNA chain | Mass: 29593.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
-Protein kinase ... , 4 types, 4 molecules GHIJ
#4: RNA chain | Mass: 9738.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pk1 / Source: (natural) Thermus thermophilus (bacteria) |
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#6: RNA chain | Mass: 18915.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pk2 / Source: (natural) Thermus thermophilus (bacteria) |
#7: RNA chain | Mass: 15808.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pk3 / Source: (natural) Thermus thermophilus (bacteria) |
#8: RNA chain | Mass: 16781.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pk4 / Source: (natural) Thermus thermophilus (bacteria) |
-Protein , 2 types, 2 molecules KY
#10: Protein | Mass: 15087.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: O66640*PLUS |
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#11: Protein | Mass: 44742.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN6*PLUS |
-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: 70S ribosome / Type: RIBOSOME |
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Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Quantifoil holley-carbon film grids |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Aug 1, 2003 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 49000 X / Calibrated magnification: 52000 X / Nominal defocus max: 1450 nm / Nominal defocus min: 3700 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
CTF correction | Details: CTF correction of 3D-maps by Wiener filtration | ||||||||||||||||||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Method: 3D projection matching: conjugate gradients with regularization Resolution: 13 Å / Num. of particles: 27644 / Actual pixel size: 2.82 Å / Magnification calibration: TMV Details: SPIDER package, This entry contains only C alpha and P atoms. Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--manual fitting in O | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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