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- PDB-3j0d: Models for the T. thermophilus ribosome recycling factor bound to... -

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Basic information

Entry
Database: PDB / ID: 3j0d
TitleModels for the T. thermophilus ribosome recycling factor bound to the E. coli post-termination complex
Components
  • (ribosomal 16S ...) x 2
  • (ribosomal 23S ...) x 6
  • 30S ribosomal protein S12
  • 50S ribosomal protein L11
  • Ribosome-recycling factor
KeywordsTRANSLATION / ribosome / ribosome recycling factor
Function / homology
Function and homology information


stringent response / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / positive regulation of RNA splicing / maintenance of translational fidelity / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly ...stringent response / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / positive regulation of RNA splicing / maintenance of translational fidelity / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / cytosol / cytoplasm
Similarity search - Function
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 ...Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein S12, bacterial-type / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS12 / Ribosome-recycling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.1 Å
AuthorsYokoyama, T. / Shaikh, T.R. / Iwakura, N. / Kaji, H. / Kaji, A. / Agrawal, R.K.
CitationJournal: EMBO J / Year: 2012
Title: Structural insights into initial and intermediate steps of the ribosome-recycling process.
Authors: Takeshi Yokoyama / Tanvir R Shaikh / Nobuhiro Iwakura / Hideko Kaji / Akira Kaji / Rajendra K Agrawal /
Abstract: The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron ...The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron microscopic structures of the PoTC·RRF complex, with and without EF-G. We find that domain II of RRF initially interacts with universally conserved residues of the 23S rRNA helices 43 and 95, and protein L11 within the 50S ribosomal subunit. Upon EF-G binding, both RRF and tRNA are driven towards the tRNA-exit (E) site, with a large rotational movement of domain II of RRF towards the 30S ribosomal subunit. During this intermediate step of the recycling process, domain II of RRF and domain IV of EF-G adopt hitherto unknown conformations. Furthermore, binding of EF-G to the PoTC·RRF complex reverts the ribosome from ratcheted to unratcheted state. These results suggest that (i) the ribosomal intersubunit reorganizations upon RRF binding and subsequent EF-G binding could be instrumental in destabilizing the PoTC and (ii) the modes of action of EF-G during tRNA translocation and ribosome-recycling steps are markedly different.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Jul 23, 2014Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 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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Structure viewerMolecule:
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Assembly

Deposited unit
A: ribosomal 23S RNA
B: ribosomal 23S RNA
C: ribosomal 23S RNA
D: ribosomal 23S RNA
E: ribosomal 23S RNA
F: ribosomal 23S RNA
G: 50S ribosomal protein L11
H: ribosomal 16S RNA
h: ribosomal 16S RNA
I: 30S ribosomal protein S12
J: Ribosome-recycling factor


Theoretical massNumber of molelcules
Total (without water)106,46111
Polymers106,46111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
DetailsTHE FULL BIOLOGICAL ASSEMBLY IS A COMPLEX OF MRNA, TRNA, RRF, AND RIBOSOME. REMARK 350 REFERS ONLY TO INDIVIDUAL CHAINS THAT WERE MODELED AND DOES NOT REPRESENT THE FULL BIOLOGICAL ASSEMBLY.

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Components

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Ribosomal 23S ... , 6 types, 6 molecules ABCDEF

#1: RNA chain ribosomal 23S RNA


Mass: 16114.632 Da / Num. of mol.: 1 / Fragment: helices 43 and 44 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.2
#2: RNA chain ribosomal 23S RNA


Mass: 6994.202 Da / Num. of mol.: 1 / Fragment: helix 69 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.2
#3: RNA chain ribosomal 23S RNA


Mass: 5459.285 Da / Num. of mol.: 1 / Fragment: helix 71 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.2
#4: RNA chain ribosomal 23S RNA


Mass: 4228.565 Da / Num. of mol.: 1 / Fragment: helix 80 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.2
#5: RNA chain ribosomal 23S RNA


Mass: 6117.697 Da / Num. of mol.: 1 / Fragment: helix 93 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.2
#6: RNA chain ribosomal 23S RNA


Mass: 6155.753 Da / Num. of mol.: 1 / Fragment: helix 95 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.2

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Protein , 3 types, 3 molecules GIJ

#7: Protein 50S ribosomal protein L11


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#10: Protein 30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3
#11: Protein Ribosome-recycling factor / RRF / Ribosome-releasing factor


Mass: 21029.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q9WX76

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Ribosomal 16S ... , 2 types, 2 molecules Hh

#8: RNA chain ribosomal 16S RNA


Mass: 5787.508 Da / Num. of mol.: 1 / Fragment: helix 44 strand 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.2
#9: RNA chain ribosomal 16S RNA


Mass: 6173.722 Da / Num. of mol.: 1 / Fragment: helix 44 strand 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: U00096.2

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Details

Sequence detailsRIBOSOMAL RNA IS ONLY PARTIALLY MODELED IN THIS ENTRY: CHAINS A-F ARE PARTS OF THE 23S RIBOSOMAL ...RIBOSOMAL RNA IS ONLY PARTIALLY MODELED IN THIS ENTRY: CHAINS A-F ARE PARTS OF THE 23S RIBOSOMAL RNA AND CHAINS H AND h ARE PARTS OF THE 16S RIBOSOMAL RNA.

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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 POST TERMINATION COMPLEX / Type: RIBOSOME / Details: POTC-TTRRF
Buffer solutionName: BUFFER R / pH: 7.5 / Details: BUFFER R
SpecimenConc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: QUANTIFOIL HOLEY CARBON FILM G
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: VITROBOT

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Dec 23, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50310 X / Nominal defocus max: 4300 nm / Nominal defocus min: 400 nm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1MDFFmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: CTF CORRECTION OF 3D MAPS BY WIENER FILTRATION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 3D PROJECTION MATCHING / Resolution: 11.1 Å / Num. of particles: 153927 / Nominal pixel size: 2.78 Å / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Details: REFINEMENT PROTOCOL--FLEXIBLE FITTING (MDFF)
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12AVY

2avy
PDB Unreleased entry

12AVY1PDBexperimental model
22AW4

2aw4
PDB Unreleased entry

12AW42PDBexperimental model
31EH1

1eh1

11EH13PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 3796 0 0 7260

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