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- PDB-3bbv: The tRNA(phe) fitted into the low resolution Cryo-EM map of the 5... -

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Basic information

Entry
Database: PDB / ID: 3bbv
TitleThe tRNA(phe) fitted into the low resolution Cryo-EM map of the 50S.nc-tRNA.Hsp15 complex
ComponentstRNA(Phe)
KeywordsRIBOSOME / PHE / tRNA / rescue stalled ribosome
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å
AuthorsJiang, L. / Abrahams, J.P.
CitationJournal: J Mol Biol / Year: 2009
Title: Recycling of aborted ribosomal 50S subunit-nascent chain-tRNA complexes by the heat shock protein Hsp15.
Authors: Linhua Jiang / Christiane Schaffitzel / Rouven Bingel-Erlenmeyer / Nenad Ban / Philipp Korber / Roman I Koning / Daniël C de Geus / Jasper R Plaisier / Jan Pieter Abrahams /
Abstract: When heat shock prematurely dissociates a translating bacterial ribosome, its 50S subunit is prevented from reinitiating protein synthesis by tRNA covalently linked to the unfinished protein chain ...When heat shock prematurely dissociates a translating bacterial ribosome, its 50S subunit is prevented from reinitiating protein synthesis by tRNA covalently linked to the unfinished protein chain that remains threaded through the exit tunnel. Hsp15, a highly upregulated bacterial heat shock protein, reactivates such dead-end complexes. Here, we show with cryo-electron microscopy reconstructions and functional assays that Hsp15 translocates the tRNA moiety from the A site to the P site of stalled 50S subunits. By stabilizing the tRNA in the P site, Hsp15 indirectly frees up the A site, allowing a release factor to land there and cleave off the tRNA. Such a release factor must be stop codon independent, suggesting a possible role for a poorly characterized class of putative release factors that are upregulated by cellular stress, lack a codon recognition domain and are conserved in eukaryotes.
History
DepositionNov 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 2.0Jul 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Feb 21, 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
z: tRNA(Phe)


Theoretical massNumber of molelcules
Total (without water)24,6501
Polymers24,6501
Non-polymers00
Water00
1


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

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Components

#1: RNA chain tRNA(Phe) / HSP15


Mass: 24649.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: part of the 50S ribosomal particle in assembly with Heat Shock Protein 15
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli)

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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: 0S.nc-tRNA.Hsp15 complex / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3.5 nm / Nominal defocus min: 1.5 nm / Cs: 2 mm
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1localfitmodel fitting
2Situsmodel fitting
3EMAN3D reconstruction
CTF correctionDetails: CTF correction of each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: cross-common lines, projection matching / Resolution: 10 Å / Nominal pixel size: 2.54 Å / Actual pixel size: 2.54 Å / Details: EMAN software / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: best visual fit, best correlation value
Details: METHOD--colores REFINEMENT PROTOCOL--multi-rigid body refinement
Atomic model buildingPDB-ID: 2OW8

2ow8
PDB Unreleased entry


Pdb chain-ID: z / Accession code: 2OW8 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1628 0 0 1628

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