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- PDB-1t1o: Components of the control 70S ribosome to provide reference for t... -

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Entry
Database: PDB / ID: 1t1o
TitleComponents of the control 70S ribosome to provide reference for the RRF binding site
Components
  • 19-mer fragment of the 23S rRNA
  • 42-mer fragment of double helix from 16S rRNA
  • dodecamer fragment of double helix from 23S rRNA
KeywordsRIBOSOME / RRF binding position on the ribosome
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsAgrawal, R.K. / Sharma, M.R. / Kiel, M.C. / Hirokawa, G. / Booth, T.M. / Spahn, C.M. / Grassucci, R.A. / Kaji, A. / Frank, J.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2004
Title: Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications.
Authors: Rajendra K Agrawal / Manjuli R Sharma / Michael C Kiel / Go Hirokawa / Timothy M Booth / Christian M T Spahn / Robert A Grassucci / Akira Kaji / Joachim Frank /
Abstract: After the termination step of protein synthesis, a deacylated tRNA and mRNA remain associated with the ribosome. The ribosome-recycling factor (RRF), together with elongation factor G (EF-G), ...After the termination step of protein synthesis, a deacylated tRNA and mRNA remain associated with the ribosome. The ribosome-recycling factor (RRF), together with elongation factor G (EF-G), disassembles this posttermination complex into mRNA, tRNA, and the ribosome. We have obtained a three-dimensional cryo-electron microscopic map of a complex of the Escherichia coli 70S ribosome and RRF. We find that RRF interacts mainly with the segments of the large ribosomal subunit's (50S) rRNA helices that are involved in the formation of two central intersubunit bridges, B2a and B3. The binding of RRF induces considerable conformational changes in some of the functional domains of the ribosome. As compared to its binding position derived previously by hydroxyl radical probing study, we find that RRF binds further inside the intersubunit space of the ribosome such that the tip of its domain I is shifted (by approximately 13 A) toward protein L5 within the central protuberance of the 50S subunit, and domain II is oriented more toward the small ribosomal subunit (30S). Overlapping binding sites of RRF, EF-G, and the P-site tRNA suggest that the binding of EF-G would trigger the removal of deacylated tRNA from the P site by moving RRF toward the ribosomal E site, and subsequent removal of mRNA may be induced by a shift in the position of 16S rRNA helix 44, which harbors part of the mRNA.
#1: Journal: Cell / Year: 2001
Title: High resolution structure of the large ribosomal subunit from a mesophilic eubacterium.
Authors: J Harms / F Schluenzen / R Zarivach / A Bashan / S Gat / I Agmon / H Bartels / F Franceschi / A Yonath /
Abstract: We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ...We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ligands. The over-all structure of D50S is similar to that from the archae bacterium Haloarcula marismortui (H50S); however, a detailed comparison revealed significant differences, for example, in the orientation of nucleotides in peptidyl transferase center and in the structures of many ribosomal proteins. Analysis of ribosomal features involved in dynamic aspects of protein biosynthesis that are partially or fully disordered in H50S revealed the conformations of intersubunit bridges in unbound subunits, suggesting how they may change upon subunit association and how movements of the L1-stalk may facilitate the exit of tRNA.
#2: Journal: Nature / Year: 2000
Title: Structure of the 30S ribosomal subunit.
Authors: B T Wimberly / D E Brodersen / W M Clemons / R J Morgan-Warren / A P Carter / C Vonrhein / T Hartsch / V Ramakrishnan /
Abstract: Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we ...Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein-RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.
History
DepositionApr 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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 / em_image_scans / 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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Assembly

Deposited unit
A: dodecamer fragment of double helix from 23S rRNA
B: 19-mer fragment of the 23S rRNA
C: 42-mer fragment of double helix from 16S rRNA


Theoretical massNumber of molelcules
Total (without water)23,5113
Polymers23,5113
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 dodecamer fragment of double helix from 23S rRNA / Coordinate model: P atoms only


Mass: 3852.344 Da / Num. of mol.: 1 / Fragment: Apical loop of Helix 43 / Source method: isolated from a natural source / Details: fitted into the cryo-EM map of the 70S ribosome / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#2: RNA chain 19-mer fragment of the 23S rRNA / Coordinate model: P atoms only


Mass: 6077.673 Da / Num. of mol.: 1 / Fragment: Helix 69 / Source method: isolated from a natural source / Details: fitted into the cryo-EM map of the 70S ribosome / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600
#3: RNA chain 42-mer fragment of double helix from 16S rRNA / Ribosome releasing factor / RRF / Coordinate model: P atoms only


Mass: 13581.124 Da / Num. of mol.: 1 / Fragment: Top portion of helix 44 / Source method: isolated from a natural source / Details: fitted into the cryo-EM map of the 70S ribosome / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600

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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: 70S-RRF complex / Type: RIBOSOME
Buffer solutionpH: 7.5
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holley-carbon film grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jun 1, 2002
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49696 X / Nominal defocus max: 4400 nm / Nominal defocus min: 1400 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

CTF correctionDetails: CTF correction of 3D-maps by Wiener filtration
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 3D projection matching; conjugate gradients with regularization
Resolution: 12 Å / Num. of particles: 51217 / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Details: METHOD--Cross corelation coefficient based manual fitting in O
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11KC9

1kc9
PDB Unreleased entry

11KC91PDBexperimental model
21JFJ

1jfj

11JFJ2PDBexperimental model
Refinement stepCycle: LAST /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 73 0 0 73

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