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- PDB-1mi6: Docking of the modified RF2 X-ray structure into the Low Resoluti... -

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Basic information

Entry
Database: PDB / ID: 1mi6
TitleDocking of the modified RF2 X-ray structure into the Low Resolution Cryo-EM map of RF2 E.coli 70S Ribosome
Componentspeptide chain release factor RF-2
KeywordsTRANSLATION / RIBOSOME / RF2 / Release Complex / Conformational Changes
Function / homology
Function and homology information


translation release factor activity, codon specific / translational termination / viral translational frameshifting / cytosol
Similarity search - Function
Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain
Similarity search - Domain/homology
Peptide chain release factor RF2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.8 Å
AuthorsRawat, U.B.S. / Zavialov, A.V. / Sengupta, J. / Valle, M. / Grassucci, R.A. / Linde, J. / Vestergaard, B. / Ehrenberg, M. / Frank, J.
Citation
Journal: Nature / Year: 2003
Title: A cryo-electron microscopic study of ribosome-bound termination factor RF2.
Authors: Urmila B S Rawat / Andrey V Zavialov / Jayati Sengupta / Mikel Valle / Robert A Grassucci / Jamie Linde / Bente Vestergaard / Måns Ehrenberg / Joachim Frank /
Abstract: Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into ...Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: The Crystal Structure of Human Eukaryotic Release Factor eRF1-Mechanism of Stop Codon Recognition and peptidyl-tRNA hydrolysis
#2: Journal: Mol.Cell / Year: 2001
Title: Bacterial Polypeptide Release Factor RF2 is structurally distinct from Eukaryotic eRF1
History
DepositionAug 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.5Feb 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 / refine / struct_ref_seq_dif
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 / _refine.ls_d_res_high / _struct_ref_seq_dif.details

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Assembly

Deposited unit
A: peptide chain release factor RF-2


Theoretical massNumber of molelcules
Total (without water)41,2571
Polymers41,2571
Non-polymers00
Water00
1


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

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Components

#1: Protein peptide chain release factor RF-2 / Release Factor 2 / RF2 / Coordinate model: Cα atoms only


Mass: 41256.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P07012

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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 - RF2(wt) Complex / Type: RIBOSOME
Buffer solutionName: polymix buffer / pH: 7.5 / Details: polymix buffer
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Rapid-freezing in liquid ethane
Crystal grow
*PLUS
Method: cryo-electron microscopy / Details: cryo-electron microscopy

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Nov 8, 2001
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: 4000 nm / Nominal defocus min: 2500 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

EM software
IDNameCategory
1Omodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: CTF correction of 3D-maps
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Reference Based Alignment / Resolution: 12.8 Å / Num. of particles: 18199 / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Details: SPIDER package / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--Manual
Atomic model buildingPDB-ID: 1GQE

1gqe


Accession code: 1GQE / Source name: PDB / Type: experimental model
RefinementStarting model: PDB entry 1GQE

1gqe


Highest resolution: 12.8 Å
Refinement stepCycle: LAST / Highest resolution: 10.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms362 0 0 0 362

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