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- PDB-1qzd: EF-Tu.kirromycin coordinates fitted into the cryo-EM map of EF-Tu... -
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Basic information
Entry | Database: PDB / ID: 1qzd | ||||||
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Title | EF-Tu.kirromycin coordinates fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome | ||||||
![]() | Elongation factor Tu | ||||||
![]() | BIOSYNTHETIC PROTEIN / Elongation factor | ||||||
Function / homology | ![]() guanyl-nucleotide exchange factor complex / translational elongation / guanosine tetraphosphate binding / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å | ||||||
![]() | Valle, M. / Zavialov, A. / Li, W. / Stagg, S.M. / Sengupta, J. / Nielsen, R.C. / Nissen, P. / Harvey, S.C. / Ehrenberg, M. / Frank, J. | ||||||
![]() | ![]() Title: Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Authors: Mikel Valle / Andrey Zavialov / Wen Li / Scott M Stagg / Jayati Sengupta / Rikke C Nielsen / Poul Nissen / Stephen C Harvey / Måns Ehrenberg / Joachim Frank / ![]() Abstract: Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, ...Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, at a resolution of approximately 9 A, showing that during the incorporation of the aa-tRNA into the 70S ribosome of Escherichia coli, the flexibility of aa-tRNA allows the initial codon recognition and its accommodation into the ribosomal A site. In addition, a conformational change observed in the GTPase-associated center (GAC) of the ribosomal 50S subunit may provide the mechanism by which the ribosome promotes a relative movement of the aa-tRNA with respect to EF-Tu. This relative rearrangement seems to facilitate codon recognition by the incoming aa-tRNA, and to provide the codon-anticodon recognition-dependent signal for the GTPase activity of EF-Tu. From these new findings we propose a mechanism that can explain the sequence of events during the decoding of mRNA on the ribosome. | ||||||
History |
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Remark 999 | SEQUENCE THE PROTEIN STRUCTURE CONTAINS CA 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 | ![]() | 24.9 KB | Display | ![]() |
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PDB format | ![]() | 11.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 785.3 KB | Display | ![]() |
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Full document | ![]() | 784.8 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1055MC ![]() 1056C ![]() 1395C ![]() 1qzaC ![]() 1qzbC ![]() 1qzcC ![]() 1r2wC ![]() 1r2xC 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: 43239.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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 |
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Sample preparation
Component |
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Buffer solution | Name: Polymix buffer / pH: 7.5 / Details: Polymix buffer | ||||||||||||
Specimen | 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 |
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: 2000 nm |
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
EM software |
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CTF correction | Details: CTF correction of 3D maps by Wiener filteration | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: 3D projection matching; conjugate gradient with regularization Resolution: 10 Å / Resolution method: OTHER / Num. of particles: 75996 / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--Manual fitting in O | ||||||||||||
Atomic model building | PDB-ID: 1OB2 Accession code: 1OB2 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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