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Yorodumi- PDB-3ep2: Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ep2 | ||||||
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Title | Model of Phe-tRNA(Phe) 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 / translational elongation / RNA folding / 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 / translational elongation / RNA folding / translation elongation factor activity / translational termination / positive regulation of RNA splicing / ribosomal large subunit assembly / maintenance of translational fidelity / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm / cytosol 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. #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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3ep2.cif.gz | 42.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ep2.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ep2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ep2_validation.pdf.gz | 840.5 KB | Display | wwPDB validaton report |
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Full document | 3ep2_full_validation.pdf.gz | 840 KB | Display | |
Data in XML | 3ep2_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 3ep2_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/3ep2 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/3ep2 | HTTPS FTP |
-Related structure data
Related structure data | 1055M 1564C 1565C 3eq3C 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(Phe), 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 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jul 1, 2002 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 49650 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: SINGLE PARTICLE / Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75996 / 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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