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Yorodumi- PDB-3eq3: Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eq3 | ||||||
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Title | Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM | ||||||
Components |
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Keywords | RIBOSOMAL 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 / guanosine tetraphosphate binding / stringent response / misfolded RNA binding / Group I intron splicing / RNA folding / translational elongation / translation elongation factor activity / translational termination / positive regulation of RNA splicing ...guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / stringent response / misfolded RNA binding / Group I intron splicing / RNA folding / translational elongation / 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 / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å | ||||||
Authors | Frank, 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3eq3.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eq3.ent.gz | 19.7 KB | Display | PDB format |
PDBx/mmJSON format | 3eq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eq3_validation.pdf.gz | 828.7 KB | Display | wwPDB validaton report |
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Full document | 3eq3_full_validation.pdf.gz | 828.1 KB | Display | |
Data in XML | 3eq3_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 3eq3_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/3eq3 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/3eq3 | HTTPS FTP |
-Related structure data
Related structure data | 1565MC 1564C 3ep2C 3eq4C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules XLI
#1: Protein | 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 |
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#2: Protein | 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 | Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: P0A7J7 |
-RNA chain , 6 types, 6 molecules YACBDE
#4: RNA chain | Mass: 23844.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) |
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#5: RNA chain | Mass: 2871.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) |
#6: RNA chain | Mass: 3601.218 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) |
#7: RNA chain | Mass: 15504.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) |
#8: RNA chain | Mass: 9089.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) |
#9: RNA chain | Mass: 5427.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ribosome in pre-accommodated state / Type: RIBOSOME Details: A/T-tRNA(Trp), EF-Tu, L11, S12, fragments h44 and h18 from the 16S rRNA, fragments H43-H44, H69, and H95 from the 23S rRNA |
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Buffer solution | pH: 7.5 Details: HiFi buffer (50 mM Tris-HCl pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2) |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: NITROGEN |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Jan 1, 2007 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GENERIC CCD |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Method: SINGLE PARTICLE / Resolution: 9 Å / Num. of particles: 290000 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: cross-correlation coefficient Details: METHOD--See Method in the citation REFINEMENT PROTOCOL--auto | |||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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