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- PDB-1lu3: Separate Fitting of the Anticodon Loop Region of tRNA (nucleotide... -

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Entry
Database: PDB / ID: 1lu3
TitleSeparate 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
ComponentsPHENYLALANINE TRANSFER RNA
KeywordsRNA / tRNA / ternary complex / cryo-EM / 70S E.coli ribosome / conformational change
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16.8 Å
AuthorsValle, M. / Sengupta, J. / Swami, N.K. / Grassucci, R.A. / Burkhardt, N. / Nierhaus, K.H. / Agrawal, R.K. / Frank, J.
Citation
Journal: EMBO J / Year: 2002
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: Journal: J.Mol.Biol. / Year: 1999
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: Journal: Science / Year: 1995
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: Journal: Nature / Year: 1997
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: Journal: Structure / Year: 1993
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: Journal: Structure / Year: 1996
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.
History
DepositionMay 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

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Assembly

Deposited unit
A: PHENYLALANINE TRANSFER RNA


Theoretical massNumber of molelcules
Total (without water)5,4661
Polymers5,4661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain PHENYLALANINE TRANSFER RNA


Mass: 5466.326 Da / Num. of mol.: 1 / Fragment: anticodon loop region / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E.coli 70S ribosome-Ternary complex-GDP-Kirromycin / Type: RIBOSOME / Details: E.coli 70S ribosome-Ternary complex-GDP-Kirromycin
Buffer solutionName: Hepes-KOH buffer at pH 7.5 / pH: 7.5 / Details: Hepes-KOH buffer at pH 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS EM420 / Date: Mar 1, 2001
Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 52000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategoryDetails
1Omodel fittingManual
2SPIDER3D reconstruction
CTF correctionDetails: CTF correction of 3D-maps
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 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 buildingProtocol: OTHER / Details: METHOD--Manual
Atomic model buildingPDB-ID: 1TTT

1ttt


Accession code: 1TTT / Source name: PDB / Type: experimental model
RefinementHighest resolution: 16.8 Å
Refinement stepCycle: LAST / Highest resolution: 16.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 365 0 0 365

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