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Yorodumi- PDB-1pn6: Domain-wise fitting of the crystal structure of T.thermophilus EF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pn6 | ||||||
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Title | Domain-wise fitting of the crystal structure of T.thermophilus EF-G into the low resolution map of the release complex.Puromycin.EFG.GDPNP of E.coli 70S ribosome. | ||||||
Components | Elongation factor G | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Elongation Factor-G / E.coli 70S ribosome / Post-termination complex / Fitting of crystal structure / Cryo-EM | ||||||
Function / homology | Function and homology information translational elongation / translation elongation factor activity / GDP binding / ribosome binding / GTPase activity / GTP binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.8 Å | ||||||
Authors | Valle, M. / Zavialov, A. / Sengupta, J. / Rawat, U. / Ehrenberg, M. / Frank, J. | ||||||
Citation | Journal: Cell / Year: 2003 Title: Locking and unlocking of ribosomal motions. Authors: Mikel Valle / Andrey Zavialov / Jayati Sengupta / Urmila Rawat / Måns Ehrenberg / Joachim Frank / Abstract: During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the ...During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the direction of the mRNA movement. By means of cryo-electron microscopy we observe that this rotation is accompanied by a 20 A movement of the L1 stalk of the 50S subunit, implying that this region is involved in the translocation of deacylated tRNAs from the P to the E site. These ribosomal motions can occur only when the P-site tRNA is deacylated. Prior to peptidyl-transfer to the A-site tRNA or peptide removal, the presence of the charged P-site tRNA locks the ribosome and prohibits both of these motions. #1: Journal: J.Mol.Biol. / Year: 2000 Title: STRUCTURE OF A MUTANT EF-G REVEALS DOMAIN III AND POSSIBLY THE FUSIDIC ACID BINDING SITE #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. #3: Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: A posttermination ribosomal complex is the guanine exchange factor for peptide reslease factor RF3. | ||||||
History |
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Remark 999 | The structure contains C alpha atoms only |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1pn6.cif.gz | 35.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pn6.ent.gz | 18.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pn6_validation.pdf.gz | 749.8 KB | Display | wwPDB validaton report |
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Full document | 1pn6_full_validation.pdf.gz | 749.4 KB | Display | |
Data in XML | 1pn6_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 1pn6_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/1pn6 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/1pn6 | HTTPS FTP |
-Related structure data
Related structure data | 1362MC 1363MC 1364MC 1365MC 1366MC 1pn7C 1pn8C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 76910.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P13551 |
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-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 |
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Buffer solution | pH: 7.5 | ||||||||||||
Specimen | Conc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Details: Quantifoil holley-carbon film grids | ||||||||||||
Vitrification | Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane | ||||||||||||
Crystal grow | *PLUS Method: electron microscopy / Details: electron microscopy |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jun 1, 2001 |
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: 49696 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 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 gradients with regularization Resolution: 10.8 Å / Actual pixel size: 2.82 Å / Magnification calibration: TMV Details: SPIDER package. CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS EF-G H573A AT 2.8A RESOLUTION. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--Manual fitting in O | ||||||||||||
Atomic model building | PDB-ID: 1FNM Accession code: 1FNM / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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