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- PDB-1pn7: Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray s... -
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Basic information
Entry | Database: PDB / ID: 1pn7 | ||||||
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Title | Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome | ||||||
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![]() | RNA binding protein/RNA / ribosomal protein / tRNA binding protein / tRNA / RNA binding protein-RNA COMPLEX | ||||||
Function / homology | ![]() small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.8 Å | ||||||
![]() | 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. | ||||||
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 | ![]() | 23.1 KB | Display | ![]() |
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PDB format | ![]() | 9.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 758.5 KB | Display | ![]() |
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Full document | ![]() | 758 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1362MC ![]() 1363MC ![]() 1364MC ![]() 1365MC ![]() 1366MC ![]() 1pn6C ![]() 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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Components
#1: RNA chain | Mass: 20016.959 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 13804.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 14294.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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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 |
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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 / 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 |
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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 70S ribosome 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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