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- PDB-2z9q: Transfer RNA in the hybrid P/E state -

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Basic information

Entry
Database: PDB / ID: 2z9q
TitleTransfer RNA in the hybrid P/E state
ComponentstRNATransfer RNA
KeywordsRNA / distorted anticodon-stem-loop / twisted CCA arm
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesThermus aquaticus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.7 Å
AuthorsFrank, J. / Li, W.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2007
Title: Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data.
Authors: Wen Li / Joachim Frank /
Abstract: Transfer RNA (tRNA) transiently occupies the hybrid P/E state (P/E-tRNA) when mRNA-tRNA are translocated in the ribosome. In this study, we characterize the structure of P/E-tRNA and its interactions ...Transfer RNA (tRNA) transiently occupies the hybrid P/E state (P/E-tRNA) when mRNA-tRNA are translocated in the ribosome. In this study, we characterize the structure of P/E-tRNA and its interactions with the ribosome by correlating the results from molecular dynamics simulations on free tRNA with the cryo-EM map of P/E-tRNA. In our approach, we show that the cryo-EM map may be interpreted as a conformational average. Along the molecular dynamics trajectories (44 ns, 18 ns, and 18 ns), some of the snapshots prove to be quite close to the observed density. In a representative structure, the CCA (3') arm is uniquely twisted, and the anticodon stem loop is kinked at the junctions to both the anticodon loop and the D stem. In addition, the map shows that the P/E-tRNA is no longer bound to helix H69 of 23S rRNA and is flexible, and the conformations of helices H68 and h44 of 16S rRNA differ from those in the x-ray structure. Thus, our study presents structural and dynamic information on the P/E-tRNA and characterizes its interactions with the translocating ribosome.
#1: Journal: Cell / Year: 2003
Title: Locking and unlocking of ribosomal motions.
Authors: Mikel Valle / Andrey Zavialov / Jayati Sengupta / Urmila Rawat / Måns Ehrenberg / Joachim Frank /
Abstract: During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the ...During the ribosomal translocation, the binding of elongation factor G (EF-G) to the pretranslocational ribosome leads to a ratchet-like rotation of the 30S subunit relative to the 50S subunit in the direction of the mRNA movement. By means of cryo-electron microscopy we observe that this rotation is accompanied by a 20 A movement of the L1 stalk of the 50S subunit, implying that this region is involved in the translocation of deacylated tRNAs from the P to the E site. These ribosomal motions can occur only when the P-site tRNA is deacylated. Prior to peptidyl-transfer to the A-site tRNA or peptide removal, the presence of the charged P-site tRNA locks the ribosome and prohibits both of these motions.
History
DepositionSep 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 11, 2019Group: Data collection / Database references / Category: database_2 / em_software / Item: _em_software.image_processing_id
Revision 1.3Mar 13, 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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Structure visualization

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Assembly

Deposited unit
A: tRNA


Theoretical massNumber of molelcules
Total (without water)24,5451
Polymers24,5451
Non-polymers00
Water0
1


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

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Components

#1: RNA chain tRNA / Transfer RNA / Coordinate model: P atoms only


Mass: 24544.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria)

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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: EF-G bound Release Complex in the presence of Puromycin and GDPNP
Type: RIBOSOME
Buffer solutionName: polymix / pH: 7.5 / Details: polymix
SpecimenConc.: 32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: carbon on quantifoil grids
VitrificationCryogen name: ETHANE / Details: PLUNGED INTO ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jun 1, 2001 / Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN
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: 3.925 nm / Nominal defocus min: 1.75 nm / Cs: 2 mm
Specimen holderTemperature: 80 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 38858
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
Details: Fast Motif Search Procedure in SPIDER. Reference: Rath and Frank 2004 JSB 145 page84
CTF correctionDetails: CTF correction of each defocus group reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: single particle reconstructionSingle particle analysis
Resolution: 11.7 Å / Nominal pixel size: 2.8 Å / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Details: THE STRUCTURE CONTAINS P ATOMS ONLY / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: cross correlation coefficient / Details: REFINEMENT PROTOCOL--auto
Atomic model buildingPDB-ID: 1TTT

1ttt


Accession code: 1TTT / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 75 0 0 75

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