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- PDB-1r2x: Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM... -

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Basic information

Entry
Database: PDB / ID: 1r2x
TitleCoordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome
Components
  • 50S ribosomal protein L11
  • 58nts of 23S rRNA
KeywordsRNA BINDING PROTEIN/RNA / rna / ribosomal protein / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsValle, M. / Zavialov, A. / Li, W. / Stagg, S.M. / Sengupta, J. / Nielsen, R.C. / Nissen, P. / Harvey, S.C. / Ehrenberg, M. / Frank, J.
CitationJournal: Nat Struct Biol / Year: 2003
Title: Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy.
Authors: Mikel Valle / Andrey Zavialov / Wen Li / Scott M Stagg / Jayati Sengupta / Rikke C Nielsen / Poul Nissen / Stephen C Harvey / Måns Ehrenberg / Joachim Frank /
Abstract: Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, ...Aminoacyl-tRNAs (aa-tRNAs) are delivered to the ribosome as part of the ternary complex of aa-tRNA, elongation factor Tu (EF-Tu) and GTP. Here, we present a cryo-electron microscopy (cryo-EM) study, at a resolution of approximately 9 A, showing that during the incorporation of the aa-tRNA into the 70S ribosome of Escherichia coli, the flexibility of aa-tRNA allows the initial codon recognition and its accommodation into the ribosomal A site. In addition, a conformational change observed in the GTPase-associated center (GAC) of the ribosomal 50S subunit may provide the mechanism by which the ribosome promotes a relative movement of the aa-tRNA with respect to EF-Tu. This relative rearrangement seems to facilitate codon recognition by the incoming aa-tRNA, and to provide the codon-anticodon recognition-dependent signal for the GTPase activity of EF-Tu. From these new findings we propose a mechanism that can explain the sequence of events during the decoding of mRNA on the ribosome.
History
DepositionSep 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 4, 2013Group: Other
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE THE PROTEIN STRUCTURE CONTAINS CA ATOMS and THE RNA STRUCTURE CONTAINS P ATOMS ONLY

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Assembly

Deposited unit
C: 58nts of 23S rRNA
A: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)33,8032
Polymers33,8032
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 58nts of 23S rRNA / Coordinate model: P atoms only


Mass: 18693.145 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein 50S ribosomal protein L11 / Coordinate model: Cα atoms only


Mass: 15109.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermotoga maritima (bacteria) / References: UniProt: P29395

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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

Component
IDNameTypeParent-IDDetails
170S ribosomeRIBOSOME0
250S ribosomal protein L111STRUCTURAL CONSTITUENT OF RIBOSOME
3A/T site tRNA1
Buffer solutionName: Polymix buffer / pH: 7.5 / Details: Polymix buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holley carbon coated grids
VitrificationCryogen name: ETHANE / Details: Rapid freezing in liquid ethane
Crystal grow
*PLUS
Method: electron microscopy / Details: electron microscopy

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 200 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Reference based alignment / Resolution: 9 Å / Num. of particles: 75996 / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Details: METHOD--manual using O
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms133 57 0 0 190

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