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- PDB-1pn6: Domain-wise fitting of the crystal structure of T.thermophilus EF... -
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Open data
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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. | ||||||
![]() | Elongation factor G![]() | ||||||
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Function / homology | ![]() ribosome disassembly / translational elongation / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Valle, M. / Zavialov, A. / Sengupta, J. / Rawat, U. / Ehrenberg, M. / Frank, J. | ||||||
![]() | ![]() 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: ![]() Title: STRUCTURE OF A MUTANT EF-G REVEALS DOMAIN III AND POSSIBLY THE FUSIDIC ACID BINDING SITE #2: ![]() Title: Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. #3: ![]() 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 |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.3 KB | Display | ![]() |
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PDB format | ![]() | 18.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1362MC ![]() 1363MC ![]() 1364MC ![]() 1365MC ![]() 1366MC ![]() 1pn7C ![]() 1pn8C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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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) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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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![]() ![]() | ||||||||||||
Specimen support | Details: Quantifoil holley-carbon film grids | ||||||||||||
Vitrification![]() | Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane | ||||||||||||
Crystal grow![]() | *PLUS Method: ![]() |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
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 |
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Processing
CTF correction![]() | Details: CTF correction of 3D-maps by Wiener filtration | ||||||||||||
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Symmetry | Point symmetry![]() | ||||||||||||
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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