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- PDB-1lu3: Separate Fitting of the Anticodon Loop Region of tRNA (nucleotide... -
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Basic information
Entry | Database: PDB / ID: 1lu3 | ||||||
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Title | Separate Fitting of the Anticodon Loop Region of tRNA (nucleotide 26-42) in the Low Resolution Cryo-EM Map of an EF-Tu Ternary Complex (GDP and Kirromycin) Bound to E. coli 70S Ribosome | ||||||
![]() | PHENYLALANINE TRANSFER RNA | ||||||
![]() | RNA / tRNA / ternary complex / cryo-EM / 70S E.coli ribosome / conformational change | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16.8 Å | ||||||
![]() | Valle, M. / Sengupta, J. / Swami, N.K. / Grassucci, R.A. / Burkhardt, N. / Nierhaus, K.H. / Agrawal, R.K. / Frank, J. | ||||||
![]() | ![]() Title: Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. Authors: Mikel Valle / Jayati Sengupta / Neil K Swami / Robert A Grassucci / Nils Burkhardt / Knud H Nierhaus / Rajendra K Agrawal / Joachim Frank / ![]() Abstract: During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and ...During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, the anticodon end of the tRNA reaches the decoding center in the 30S subunit. Here we present the cryo- electron microscopy (EM) study of an Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic, kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new conformation that appears to facilitate the initial codon-anticodon interaction. Furthermore, the elbow region of the tRNA is seen to contact the GTPase-associated center on the 50S subunit of the ribosome, suggesting an active role of the tRNA in the transmission of the signal prompting the GTP hydrolysis upon codon recognition. #1: ![]() Title: Crystal structure of intact elongation factor EF-Tu from E.coli in GDP conformation at 2.05A resolution Authors: Song, H. / Parsons, M.R. / Rowsell, S. / Leonard, G. / Phillips, S.E. #2: ![]() Title: Crystal structure of the ternary complex of the Phe-tRNAPhe, EF-Tu, and a GTP analog Authors: Nissen, P. / Kjeldgaard, M. / Thirup, S. / Polekhina, G. / Reshetnikova, L. / Clark, B.F.C. / Nyborg, J. #3: ![]() Title: Visualization of elongation factor Tu on E.coli ribosome Authors: Stark, H. / Rodnina, M.V. / Rinke-Appel, J. / Brimacombe, R. / Wintermeyer, W. / van Heel, M. #4: ![]() Title: The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation Authors: Kjeldgaard, M. / Nissen, P. / Thirup, S. / Nyborg, J. #5: ![]() Title: Helix unwinding in the effector region of elongation factor EF-Tu-GDP Authors: Polekhina, G. / Thirup, S. / Kjeldgaard, M. / Nissen, P. / Lippmann, C. / Nyborg, J. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 20.8 KB | Display | ![]() |
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PDB format | ![]() | 10.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 729.3 KB | Display | ![]() |
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Full document | ![]() | 752.5 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1045MC ![]() 1ls2C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: RNA chain | Mass: 5466.326 Da / Num. of mol.: 1 / Fragment: anticodon loop region / 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 | Name: E.coli 70S ribosome-Ternary complex-GDP-Kirromycin / Type: RIBOSOME / Details: E.coli 70S ribosome-Ternary complex-GDP-Kirromycin |
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Buffer solution | Name: Hepes-KOH buffer at pH 7.5 / pH: 7.5 / Details: Hepes-KOH buffer at pH 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane |
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Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS EM420 / Date: Mar 1, 2001 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 52000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 10 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 | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: reference based alignment / Resolution: 16.8 Å / Num. of particles: 7985 / Actual pixel size: 2.69 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Details: METHOD--Manual | ||||||||||||
Atomic model building | PDB-ID: 1TTT Accession code: 1TTT / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 16.8 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 16.8 Å
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