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- PDB-2fvo: Docking of the modified RF1 X-ray structure into the Low Resoluti... -

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Basic information

Entry
Database: PDB / ID: 2fvo
TitleDocking of the modified RF1 X-ray structure into the Low Resolution Cryo-EM map of E.coli 70S Ribosome bound with RF1
ComponentsPeptide chain release factor 1
KeywordsTRANSLATION / RF1 ribosome cryo-EM
Function / homology
Function and homology information


translation release factor activity, codon specific / cytoplasm
Similarity search - Function
Peptide chain release factor 1 / 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 1
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.8 Å
AuthorsRawat, U. / Gao, H. / Zavialov, A. / Gursky, R. / Ehrenberg, M. / Frank, J.
Citation
Journal: J Mol Biol / Year: 2006
Title: Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM.
Authors: Urmila Rawat / Haixiao Gao / Andrey Zavialov / Richard Gursky / Måns Ehrenberg / Joachim Frank /
Abstract: In eubacteria, termination of translation is signaled by any one of the stop codons UAA, UAG, and UGA moving into the ribosomal A site. Two release factors, RF1 and RF2, recognize and bind to the ...In eubacteria, termination of translation is signaled by any one of the stop codons UAA, UAG, and UGA moving into the ribosomal A site. Two release factors, RF1 and RF2, recognize and bind to the stop codons with different affinities and trigger the hydrolysis of the ester bond that links the polypeptide with the P-site tRNA. Cryo-electron microscopy (cryo-EM) results obtained in this study show that ribosome-bound RF1 is in an open conformation, unlike the closed conformation observed in the crystal structure of the free factor, allowing its simultaneous access to both the decoding center and the peptidyl-transferase center. These results are similar to those obtained for RF2, but there is an important difference in how the factors bind to protein L11, which forms part of the GTPase-associated center of the large ribosomal subunit. The difference in the binding position, C-terminal domain for RF2 versus N-terminal domain for RF1, explains a body of L11 mutation studies that revealed differential effects on the activity of the two factors. Very recent data obtained with small-angle X-ray scattering now reveal that the solution structure of RF1 is open, as here seen on the ribosome by cryo-EM, and not closed, as seen in the crystal.
#1: Journal: J Mol Biol / Year: 2004
Title: Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome.
Authors: Dong Hae Shin / Jeroen Brandsen / Jaru Jancarik / Hisao Yokota / Rosalind Kim / Sung-Hou Kim /
Abstract: We have determined the crystal structure of peptide chain release factor 1 (RF1) from Thermotoga maritima (gi 4981173) at 2.65 Angstrom resolution by selenomethionine single-wavelength anomalous ...We have determined the crystal structure of peptide chain release factor 1 (RF1) from Thermotoga maritima (gi 4981173) at 2.65 Angstrom resolution by selenomethionine single-wavelength anomalous dispersion (SAD) techniques. RF1 is a protein that recognizes stop codons and promotes the release of a nascent polypeptide from tRNA on the ribosome. Selenomethionine-labeled RF1 crystallized in space group P2(1) with three monomers per asymmetric unit. It has approximate dimensions of 75 Angstrom x 70 Angstrom x 45 Angstrom and is composed of four domains. The overall fold of each RF1 domain shows almost the same topology with Escherichia coli RF2, except that the RF1 N-terminal domain is shorter and the C-terminal domain is longer than that of RF2. The N-terminal domain of RF1 indicates a rigid-body movement relative to that of RF2 with an angle of approximately 90 degrees. Including these features, RF1 has a tripeptide anticodon PVT motif instead of the SPF motif of RF2, which confers the specificity towards the stop codons. The analyses of three molecules in the asymmetric unit and comparison with RF2 revealed the presence of dynamic movement of domains I and III, which are anchored to the central domain by hinge loops. The crystal structure of RF1 elucidates the intrinsic property of this family of having large domain movements for proper function with the ribosome.
History
DepositionJan 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: 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 1.4Feb 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

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Assembly

Deposited unit
A: Peptide chain release factor 1


Theoretical massNumber of molelcules
Total (without water)38,8441
Polymers38,8441
Non-polymers00
Water0
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 1 / RF-1 / Coordinate model: Cα atoms only


Mass: 38843.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: prfA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X183

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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 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
Specimen supportDetails: quanti-foil grids coated with a thin carbon layer
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: Dec 1, 2002
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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

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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: Single particleSingle particle analysis / Resolution: 12.8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 24622 / Actual pixel size: 2.82 Å / Magnification calibration: TMV
Details: Coordinates contain CA atoms only. ALl the image processing was done in SPIDER. 0.5 cutoff of FSC
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--Manual
Atomic model buildingPDB-ID: 1RQ0

1rq0


Accession code: 1RQ0 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 12.8 Å / Details: Coordinates contain CA atoms only
Refinement stepCycle: LAST / Highest resolution: 12.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms314 0 0 0 314

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