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- PDB-3ep2: Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state re... -

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Basic information

Entry
Database: PDB / ID: 3ep2
TitleModel of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM
Components
  • 30S ribosomal protein S12
  • 50S ribosomal protein L11
  • Elongation factor Tu
  • Fragment H43-44 of the 23S rRNA
  • Fragment H69 of the 23S rRNA
  • Fragment H95 of the 23S rRNA
  • Fragment h18 of the 16S rRNA
  • Fragment h44 of the 16S rRNA
  • tRNA
KeywordsRIBOSOMAL PROTEIN/RNA / protein translation / ternary complex / A/T-tRNA / automated data collection / Antibiotic resistance / Elongation factor / GTP-binding / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Protein biosynthesis / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / RIBOSOMAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / stringent response / translational elongation / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / translational termination ...guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / stringent response / translational elongation / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / translational termination / positive regulation of RNA splicing / maintenance of translational fidelity / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 ...Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L11, bacterial-type / 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. / 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/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein S12, bacterial-type / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Elongation factor Tu 1 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS12 / Elongation factor Tu 2
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsFrank, J. / Li, W. / Agirrezabala, X.
Citation
Journal: EMBO J / Year: 2008
Title: Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
Authors: Wen Li / Xabier Agirrezabala / Jianlin Lei / Lamine Bouakaz / Julie L Brunelle / Rodrigo F Ortiz-Meoz / Rachel Green / Suparna Sanyal / Måns Ehrenberg / Joachim Frank /
Abstract: The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes ...The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes of different aa-tRNAs, we compared cryo-EM maps of the kirromycin-stalled ribosome bound with ternary complexes containing Phe-tRNA(Phe), Trp-tRNA(Trp), or Leu-tRNA(LeuI). The three maps suggest a common binding manner of cognate aa-tRNAs in their specific binding with both the ribosome and EF-Tu. All three aa-tRNAs have the same 'loaded spring' conformation with a kink and twist between the D-stem and anticodon stem. The three complexes are similarly integrated in an interaction network, extending from the anticodon loop through h44 and protein S12 to the EF-Tu-binding CCA end of aa-tRNA, proposed to signal cognate codon-anticodon interaction to the GTPase centre and tune the accuracy of aa-tRNA selection.
#2: Journal: Nat. Struct. Molec. Biol. / Year: 2003
Title: Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy
Authors: Valle, M. / Zavialov, A. / Li, W. / Stagg, S.M. / Sengupta, J. / Nielsen, R.C. / Nissen, P. / Harvey, S.C. / Ehrenberg, M. / Frank, J.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Refinement description
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 21, 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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  • EMDB-1055
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Structure viewerMolecule:
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Assembly

Deposited unit
X: Elongation factor Tu
L: 30S ribosomal protein S12
I: 50S ribosomal protein L11
Y: tRNA
A: Fragment h18 of the 16S rRNA
C: Fragment h44 of the 16S rRNA
B: Fragment H43-44 of the 23S rRNA
D: Fragment H95 of the 23S rRNA
E: Fragment H69 of the 23S rRNA


Theoretical massNumber of molelcules
Total (without water)131,9789
Polymers131,9789
Non-polymers00
Water00
1


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

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Components

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Protein , 3 types, 3 molecules XLI

#1: Protein Elongation factor Tu / EF-Tu / P-43 / Coordinate model: Cα atoms only


Mass: 43239.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: P0A6N1, UniProt: P0CE48*PLUS
#2: Protein 30S ribosomal protein S12 / Coordinate model: Cα atoms only


Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: P0A7S3
#3: Protein 50S ribosomal protein L11 / Coordinate model: Cα atoms only


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: P0A7J7

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RNA chain , 6 types, 6 molecules YACBDE

#4: RNA chain tRNA / Coordinate model: P atoms only


Mass: 23844.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria)
#5: RNA chain Fragment h18 of the 16S rRNA / Coordinate model: P atoms only


Mass: 2871.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria)
#6: RNA chain Fragment h44 of the 16S rRNA / Coordinate model: P atoms only


Mass: 3601.218 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria)
#7: RNA chain Fragment H43-44 of the 23S rRNA / Coordinate model: P atoms only


Mass: 15504.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria)
#8: RNA chain Fragment H95 of the 23S rRNA / Coordinate model: P atoms only


Mass: 9089.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria)
#9: RNA chain Fragment H69 of the 23S rRNA / Coordinate model: P atoms only


Mass: 5427.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (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: ribosome in pre-accommodated state / Type: RIBOSOME
Details: A/T-tRNA(Phe), EF-Tu, L11, S12, fragments h44 and h18 from the 16S rRNA, fragments H43-H44, H69, and H95 from the 23S rRNA
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jul 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: 49650 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategoryDetails
1RSRefmodel fittingTNT
2SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: SINGLE PARTICLE / Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75996 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: cross-correlation coefficient
Details: METHOD--See Method in the citation REFINEMENT PROTOCOL--auto
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12AVY

2avy
PDB Unreleased entry

12AVY1PDBexperimental model
22AW4

2aw4
PDB Unreleased entry

12AW42PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms657 187 0 0 844

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