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- PDB-1qzc: Coordinates of S12, SH44, LH69 and SRL separately fitted into the... -

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Basic information

Entry
Database: PDB / ID: 1qzc
TitleCoordinates of S12, SH44, LH69 and SRL separately fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome
Components
  • (23S rRNA) x 2
  • 16S rRNA
  • 30S ribosomal protein S12
KeywordsRNA Binding Protein/RNA / ribosomal protein / rRNA / RNA Binding Protein-RNA COMPLEX
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein S12, bacterial-type / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus (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 16, 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 1.3Jul 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
Remark 999SEQUENCE THE PROTEIN STRUCTURE CONTAINS CA ATOMS and THE RNA STRUCTURES CONTAIN P ATOMS ONLY

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Assembly

Deposited unit
A: 16S rRNA
B: 23S rRNA
C: 23S rRNA
L: 30S ribosomal protein S12


Theoretical massNumber of molelcules
Total (without water)44,2154
Polymers44,2154
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 16S rRNA / Coordinate model: P atoms only


Mass: 14245.544 Da / Num. of mol.: 1 / Fragment: helix 44 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600
#2: RNA chain 23S rRNA / Coordinate model: P atoms only


Mass: 6688.036 Da / Num. of mol.: 1 / Fragment: helix 69 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600
#3: RNA chain 23S rRNA / Coordinate model: P atoms only


Mass: 8775.319 Da / Num. of mol.: 1 / Fragment: Sarcin/ricin loop (SRL) / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE 600
#4: Protein 30S ribosomal protein S12 / Coordinate model: Cα atoms only


Mass: 14506.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN3

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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
230S ribosomal protein S121structural constituent of ribosome
316S rRNA1
423S rRNA1
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: Quantifoil holley carbon film 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 / Calibrated magnification: 49696 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: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: CTF correction of 3D maps by Wiener filteration
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 3D projection matching; conjugate gradient with regularization
Resolution: 9 Å / Num. of particles: 52181 / Actual pixel size: 2.82 Å / Magnification calibration: TMV / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--Manual fitting in O
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11FFK

1ffk

11FFK1PDBexperimental model
21IBM

1ibm

11IBM2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms124 91 0 0 215

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