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- PDB-1zn1: Coordinates of RRF fitted into Cryo-EM map of the 70S post-termin... -

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Basic information

Entry
Database: PDB / ID: 1zn1
TitleCoordinates of RRF fitted into Cryo-EM map of the 70S post-termination complex
Components
  • 30S ribosomal protein S12
  • Ribosome recycling factor
  • ribosomal 16S RNA
  • ribosomal 23S RNA
KeywordsBIOSYNTHETIC/structural protein/RNA / ribosome recycling factor / elongation factor G / 70S / post-termination complex / BIOSYNTHETIC-structural protein-RNA COMPLEX
Function / homology
Function and homology information


cytoplasmic translational termination / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding ...cytoplasmic translational termination / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / cytoplasmic translation / 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 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) / Small ribosomal subunit protein uS12 / Ribosome-recycling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14.1 Å
AuthorsGao, N. / Zavialov, A.V. / Li, W. / Sengupta, J. / Valle, M. / Gursky, R.P. / Ehrenberg, M. / Frank, J.
Citation
Journal: Mol Cell / Year: 2005
Title: Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Authors: Ning Gao / Andrey V Zavialov / Wen Li / Jayati Sengupta / Mikel Valle / Richard P Gursky / Måns Ehrenberg / Joachim Frank /
Abstract: Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In ...Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In eubacteria, recycling is catalyzed by RRF (ribosome recycling factor) and EF-G (elongation factor G). By using cryo-electron microscopy, we have obtained two density maps, one of the RRF bound posttermination complex and one of the 50S subunit bound with both EF-G and RRF. Comparing the two maps, we found domain I of RRF to be in the same orientation, while domain II in the EF-G-containing 50S subunit is extensively rotated (approximately 60 degrees) compared to its orientation in the 70S complex. Mapping the 50S conformation of RRF onto the 70S posttermination complex suggests that it can disrupt the intersubunit bridges B2a and B3, and thus effect a separation of the two subunits. These observations provide the structural basis for the mechanism by which the posttermination complex is split into subunits by the joint action of RRF and EF-G.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Locking and unlocking of ribosomal motions
Authors: Valle, M. / Zavialov, A. / Sengupta, J. / Rawat, U. / Ehrenberg, M. / Frank, J.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Study of structural dynamics of E.coli 70S ribosome using real-space refinement
Authors: Gao, H. / Sengupta, J. / Valle, M. / Korostelev, A. / Eswar, N. / Stagg, S.M. / Van Roey, P. / Agrawal, R.K. / Harvey, S.C. / Sali, A. / Chapman, M.S. / Frank, J.
#3: Journal: Embo J. / Year: 2000
Title: Crystal structure of the ribosome recycling factor from E.coli
Authors: Kim, K.K. / Min, K. / Suh, S.W.
History
DepositionMay 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Data collection / Database references / Category: citation_author / em_image_scans / Item: _citation_author.name
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
Remark 999SEQUENCE This entry contains C alpha and P atoms only.

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Assembly

Deposited unit
B: ribosomal 23S RNA
C: ribosomal 16S RNA
A: Ribosome recycling factor
L: 30S ribosomal protein S12


Theoretical massNumber of molelcules
Total (without water)63,4414
Polymers63,4414
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 ribosomal 23S RNA / Coordinate model: P atoms only


Mass: 18952.248 Da / Num. of mol.: 1 / Fragment: fragment of large subunit rRNA helix 69-71 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain ribosomal 16S RNA / Coordinate model: P atoms only


Mass: 12988.728 Da / Num. of mol.: 1 / Fragment: fragment of small subunit rRNA helix 44 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Protein Ribosome recycling factor / Ribosome releasing factor / RRF / Coordinate model: Cα atoms only


Mass: 20671.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A805
#4: Protein 30S ribosomal protein S12 / Coordinate model: Cα atoms only


Mass: 10828.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3

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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 ribosome / Type: RIBOSOME
Buffer solutionName: Polymix buffer / pH: 7.5 / Details: Polymix buffer
SpecimenConc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holey 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: Feb 1, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49700 X / Nominal defocus max: -3.8 nm / Nominal defocus min: -1.4 nm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 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 gradient with regularization
Resolution: 14.1 Å / Num. of particles: 37379 / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--Manual fitting in O
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11P6G

1p6g
PDB Unreleased entry

11P6G1PDBexperimental model
21P85

1p85
PDB Unreleased entry

11P852PDBexperimental model
31EK8

1ek8

11EK83PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms282 99 0 0 381

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