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- PDB-2o0f: Docking of the modified RF3 X-ray structure into cryo-EM map of E... -

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Basic information

Entry
Database: PDB / ID: 2o0f
TitleDocking of the modified RF3 X-ray structure into cryo-EM map of E.coli 70S ribosome bound with RF3
ComponentsPeptide chain release factor 3
KeywordsTRANSLATION / RF3 / Ribosome / cryo-EM
Function / homology
Function and homology information


regulation of translational termination / translation release factor activity, codon specific / translation release factor activity, codon nonspecific / guanosine tetraphosphate binding / translational termination / maintenance of translational fidelity / GDP binding / GTPase activity / GTP binding / cytoplasm / cytosol
Similarity search - Function
Peptide chain release factor 3, C-terminal / Peptide chain release factor 3, domain III superfamily / Peptide chain release factor 3, GTP-binding domain / Class II release factor RF3, C-terminal domain / Peptide chain release factor 3 / : / Elongation factor G domain 2 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. ...Peptide chain release factor 3, C-terminal / Peptide chain release factor 3, domain III superfamily / Peptide chain release factor 3, GTP-binding domain / Class II release factor RF3, C-terminal domain / Peptide chain release factor 3 / : / Elongation factor G domain 2 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Peptide chain release factor RF3 / Peptide chain release factor 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15.5 Å
AuthorsGao, H. / Zhou, Z. / Rawat, U. / Huang, C. / Bouakaz, L. / Wang, C. / Liu, Y. / Zavialov, A. / Gursky, R. / Sanyal, S. ...Gao, H. / Zhou, Z. / Rawat, U. / Huang, C. / Bouakaz, L. / Wang, C. / Liu, Y. / Zavialov, A. / Gursky, R. / Sanyal, S. / Ehrenberg, M. / Frank, J. / Song, H.
CitationJournal: Cell / Year: 2007
Title: RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors.
Authors: Haixiao Gao / Zhihong Zhou / Urmila Rawat / Chenhui Huang / Lamine Bouakaz / Chernhoe Wang / Zhihong Cheng / Yuying Liu / Andrey Zavialov / Richard Gursky / Suparna Sanyal / Måns Ehrenberg ...Authors: Haixiao Gao / Zhihong Zhou / Urmila Rawat / Chenhui Huang / Lamine Bouakaz / Chernhoe Wang / Zhihong Cheng / Yuying Liu / Andrey Zavialov / Richard Gursky / Suparna Sanyal / Måns Ehrenberg / Joachim Frank / Haiwei Song /
Abstract: During translation termination, class II release factor RF3 binds to the ribosome to promote rapid dissociation of a class I release factor (RF) in a GTP-dependent manner. We present the crystal ...During translation termination, class II release factor RF3 binds to the ribosome to promote rapid dissociation of a class I release factor (RF) in a GTP-dependent manner. We present the crystal structure of E. coli RF3*GDP, which has a three-domain architecture strikingly similar to the structure of EF-Tu*GTP. Biochemical data on RF3 mutants show that a surface region involving domains II and III is important for distinct steps in the action cycle of RF3. Furthermore, we present a cryo-electron microscopy (cryo-EM) structure of the posttermination ribosome bound with RF3 in the GTP form. Our data show that RF3*GTP binding induces large conformational changes in the ribosome, which break the interactions of the class I RF with both the decoding center and the GTPase-associated center of the ribosome, apparently leading to the release of the class I RF.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Dec 27, 2023Group: 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
A: Peptide chain release factor 3


Theoretical massNumber of molelcules
Total (without water)59,6521
Polymers59,6521
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 3 / RF-3 / Coordinate model: Cα atoms only


Mass: 59651.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q0T8T9, UniProt: P0A7I4*PLUS

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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: ribosomal release complex bound with RF3 / Type: RIBOSOME
Buffer solutionName: Polymix Buffer / pH: 7.5 / Details: Polymix Buffer
SpecimenConc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quanti-foil grids coated with a thin carbon layer
VitrificationInstrument: FEI VITROBOT MARK I / 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: Jan 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: 4000 nm / Nominal defocus min: 2000 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1RSRefmodel fitting
2RSRefmodel fittingTNT
3SPIDER3D reconstruction
CTF correctionDetails: CTF correction of 3D map
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single particle, Reference-based alignment / Resolution: 15.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 45000 / Nominal pixel size: 2.8 Å / Actual pixel size: 2.82 Å / Magnification calibration: TMV
Details: SPIDER package, 0.5 cutoff of FSC, This entry contains CA atoms only
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: cross-correlation coefficient
Details: METHOD--auto REFINEMENT PROTOCOL--Multi-rigid body, real-space refinement
Atomic model buildingPDB-ID: 2H5E

2h5e


Accession code: 2H5E / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms488 0 0 0 488

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