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- PDB-1ls2: Fitting of EF-Tu and tRNA in the Low Resolution Cryo-EM Map of an... -

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Basic information

Entry
Database: PDB / ID: 1ls2
TitleFitting of EF-Tu and tRNA in the Low Resolution Cryo-EM Map of an EF-Tu Ternary Complex (GDP and Kirromycin) Bound to E. coli 70S Ribosome
Components
  • Elongation Factor TuEF-Tu
  • Phenylalanine transfer RNA
KeywordsTRANSLATION/RNA / EF-Tu / ternary complex / cryo-EM / 70S E.coli ribosome / TRANSLATION-RNA COMPLEX
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Elongation factor Tu 1 / Elongation factor Tu 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Escherichia coli (E. coli)
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 Escherichia 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 16, 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 / 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
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

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Structure visualization

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Assembly

Deposited unit
B: Phenylalanine transfer RNA
A: Elongation Factor Tu


Theoretical massNumber of molelcules
Total (without water)67,7582
Polymers67,7582
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 / Coordinate model: P atoms only


Mass: 24518.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#2: Protein Elongation Factor Tu / EF-Tu / EF-Tu / P-43 / Coordinate model: Cα atoms only


Mass: 43239.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6N1, UniProt: P0CE48*PLUS

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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
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

SoftwareName: O / Classification: model building
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 / Space: REAL / Details: METHOD--Manual
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11EFC

1efc

11EFC1PDBexperimental model
21TTT

1ttt

11TTT2PDBexperimental model
RefinementHighest resolution: 16.8 Å
Refinement stepCycle: LAST / Highest resolution: 16.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms386 76 0 0 462

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