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Yorodumi- PDB-1zn0: Coordinates of RRF and EF-G fitted into Cryo-EM map of the 50S su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zn0 | ||||||
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Title | Coordinates of RRF and EF-G fitted into Cryo-EM map of the 50S subunit bound with both EF-G (GDPNP) and RRF | ||||||
Components |
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Keywords | TRANSLATION/BIOSYNTHETIC PROTEIN/RNA / ribosome recycling factor / elongation factor G / 50S subunit / TRANSLATION-BIOSYNTHETIC PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information cytoplasmic translational termination / ribosomal large subunit binding / translation / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15.5 Å | ||||||
Authors | Gao, N. / Zavialov, A.V. / Li, W. / Sengupta, J. / Valle, M. / Gursky, R.P. / Ehrenberg, M. / Frank, J. | ||||||
Citation | Journal: Mol Cell / Year: 2005 Title: Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Authors: Ning Gao / Andrey V Zavialov / Wen Li / Jayati Sengupta / Mikel Valle / Richard P Gursky / Måns Ehrenberg / Joachim Frank / Abstract: Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In ...Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In eubacteria, recycling is catalyzed by RRF (ribosome recycling factor) and EF-G (elongation factor G). By using cryo-electron microscopy, we have obtained two density maps, one of the RRF bound posttermination complex and one of the 50S subunit bound with both EF-G and RRF. Comparing the two maps, we found domain I of RRF to be in the same orientation, while domain II in the EF-G-containing 50S subunit is extensively rotated (approximately 60 degrees) compared to its orientation in the 70S complex. Mapping the 50S conformation of RRF onto the 70S posttermination complex suggests that it can disrupt the intersubunit bridges B2a and B3, and thus effect a separation of the two subunits. These observations provide the structural basis for the mechanism by which the posttermination complex is split into subunits by the joint action of RRF and EF-G. #1: Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Locking and unlocking of ribosomal motions Authors: Valle, M. / Zavialov, A. / Sengupta, J. / Rawat, U. / Ehrenberg, M. / Frank, J. #2: Journal: Embo J. / Year: 2000 Title: Crystal structure of the ribosome recycling factor from E.coli Authors: Kim, K.K. / Min, K. / Suh, S.W. | ||||||
History |
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Remark 999 | SEQUENCE This entry contains C alpha and P atoms only The sequence of this protein matches to ...SEQUENCE This entry contains C alpha and P atoms only The sequence of this protein matches to THERMUS THERMOPHILUS of pdb entry 1PN6 |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1zn0.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zn0.ent.gz | 22.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zn0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zn0_validation.pdf.gz | 785.9 KB | Display | wwPDB validaton report |
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Full document | 1zn0_full_validation.pdf.gz | 785.4 KB | Display | |
Data in XML | 1zn0_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1zn0_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/1zn0 ftp://data.pdbj.org/pub/pdb/validation_reports/zn/1zn0 | HTTPS FTP |
-Related structure data
Related structure data | 1127MC 1128MC 1zn1C 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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-Components
#1: RNA chain | Mass: 12988.728 Da / Num. of mol.: 1 / Fragment: Fragment of helix 44 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#2: Protein | Mass: 20671.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A805 |
#3: Protein | Mass: 72921.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
-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: 50S Ribosomal Subunit / Type: RIBOSOME |
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Buffer solution | Name: Polymix buffer / pH: 7.5 / Details: Polymix buffer |
Specimen | Conc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Quantifoil holey 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: Feb 1, 2003 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49700 X / Nominal defocus max: -4.8 nm / Nominal defocus min: -1.5 nm |
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 |
-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 gradient with regularization Resolution: 15.5 Å / Num. of particles: 32171 / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Details: SPIDER package / 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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