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- EMDB-1849: Cognate 70S-TC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-1849
TitleCognate 70S-TC complex
Map data
SampleCognate 70S-TC complex:
ribosome-prokaryote / (nucleic-acidNucleic acid) x 2 / EF-Tu
Keywordsribosome / ternary complex / cognate
Function / homology
Function and homology information


translational elongation / stringent response / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity ...translational elongation / stringent response / ornithine decarboxylase inhibitor activity / misfolded RNA binding / RNA folding / Group I intron splicing / transcription antitermination factor activity, RNA binding / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / transcription antitermination / translation elongation factor activity / negative regulation of translational initiation / four-way junction DNA binding / maturation of LSU-rRNA / mature ribosome assembly / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / positive regulation of RNA splicing / translational initiation / ribosome assembly / assembly of large subunit precursor of preribosome / endodeoxyribonuclease activity / DNA-templated transcription, termination / response to reactive oxygen species / maintenance of translational fidelity / positive regulation of translational fidelity / translational termination / regulation of cell growth / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / regulation of translation / 5S rRNA binding / ribosome biogenesis / response to radiation / cytosolic small ribosomal subunit / regulation of mRNA stability / small ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / GTPase activity / mRNA binding / response to antibiotic / GTP binding / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / membrane / plasma membrane / cytosol
Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L19, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / K homology domain-like, alpha/beta / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site ...Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L19, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / K homology domain-like, alpha/beta / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein S5, N-terminal / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L25/L23 / Ribosomal protein S17, conserved site / Ribosomal protein L30, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S19, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L13 / Ribosomal protein L13, bacterial-type / KOW / Ribosomal protein L24/L26, conserved site / Ribosomal protein L1, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S12/S23 / 50S ribosomal protein uL4 / Ribosomal protein L11, bacterial-type / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / K homology domain superfamily, prokaryotic type / Ribosomal protein L9/RNase H1, N-terminal / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L14P, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein L22/L17 superfamily / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L4 domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L31 type A / Ribosomal protein L21-like / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L25 / Ribosomal protein L15 / Tr-type G domain, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Elongation factor Tu, domain 2 / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L13, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein L11, N-terminal / 30S ribosomal protein S17 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25, short-form / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L9, C-terminal
30S ribosomal protein S9 / 50S ribosomal protein L6 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 30S ribosomal protein S8 / 50S ribosomal protein L13 ...30S ribosomal protein S9 / 50S ribosomal protein L6 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 30S ribosomal protein S8 / 50S ribosomal protein L13 / Elongation factor Tu 2 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / 50S ribosomal protein L18 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 30S ribosomal protein S21 / 50S ribosomal protein L25 / 30S ribosomal protein S4 / 30S ribosomal protein S5 / 50S ribosomal protein L34 / 30S ribosomal protein S3 / 50S ribosomal protein L31 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 50S ribosomal protein L15 / 50S ribosomal protein L11 / 50S ribosomal protein L19 / 50S ribosomal protein L1 / 50S ribosomal protein L20 / 50S ribosomal protein L27 / 50S ribosomal protein L28 / 50S ribosomal protein L29 / 50S ribosomal protein L32 / 30S ribosomal protein S2 / 50S ribosomal protein L33 / 50S ribosomal protein L35 / 50S ribosomal protein L9 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S16 / 30S ribosomal protein S18 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / 30S ribosomal protein S15
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.25 Å
AuthorsAgirrezabala X / Schreiner E / Trabuco LG / Lei J / Ortiz-Meoz RF / Schulten K / Green R / Frank J
CitationJournal: EMBO J / Year: 2011
Title: Structural insights into cognate versus near-cognate discrimination during decoding.
Authors: Xabier Agirrezabala / Eduard Schreiner / Leonardo G Trabuco / Jianlin Lei / Rodrigo F Ortiz-Meoz / Klaus Schulten / Rachel Green / Joachim Frank /
Abstract: The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near- ...The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA(Trp) in the presence of kirromycin. Going through more than 350 000 images and employing image classification procedures, we find ∼8% in which the TC is bound to the ribosome. The reconstructed 3D map provides a means to characterize the arrangement of the near-cognate aa-tRNA with respect to elongation factor Tu (EF-Tu) and the ribosome, as well as the domain movements of the ribosome. One of the interesting findings is that near-cognate tRNA's acceptor stem region is flexible and CCA end becomes disordered. The data bring direct structural insights into the induced-fit mechanism of decoding by the ribosome, as the analysis of the interactions between small and large ribosomal subunit, aa-tRNA and EF-Tu and comparison with the cognate case (UGG codon) offers clues on how the conformational signals conveyed to the GTPase differ in the two cases.
Validation ReportSummary, Full report, XML, About validation report
History
SupersessionID: EMD-1565
DepositionDec 13, 2010-
Header (metadata) releaseFeb 17, 2011-
Map releaseMay 6, 2011-
UpdateJan 23, 2013-
Current statusJan 23, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 32.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 32.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4v6k
  • Surface level: 32.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1849.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 250 pix.
= 375. Å
1.5 Å/pix.
x 250 pix.
= 375. Å
1.5 Å/pix.
x 250 pix.
= 375. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density
Contour LevelBy AUTHOR: 32.399999999999999 / Movie #1: 32.4
Minimum - Maximum-102.403999999999996 - 299.406000000000006
Average (Standard dev.)5.38026 (±28.487200000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-125-125-125
Dimensions250250250
Spacing250250250
CellA=B=C: 375 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z375.000375.000375.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS-125-125-125
NC/NR/NS250250250
D min/max/mean-102.404299.4065.380

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Supplemental data

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Sample components

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Entire Cognate 70S-TC complex

EntireName: Cognate 70S-TC complex
Details: 70S.fMet-tRNAfMet.EF-Tu.Trp-tRNATrp on cognate codon
Number of components: 4 / Oligomeric State: Monomeric
MassTheoretical: 2.8 MDa / Measured by: Sedimentation

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Component #1: ribosome-prokaryote, 70S Ribosome

Ribosome-prokaryoteName: 70S RibosomeRibosome / Prokaryote: ALL / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #2: nucleic-acid, fMet-tRNAfMet

nucleic acidName: fMet-tRNAfMet / a.k.a: fMet-tRNAfMet / Class: T-RNA / Structure: SINGLE STRANDED
Sequence:
CGCGGGGTGG AGCAGCCTGG TAGCTCGTCG GGCTCATAAC CCGAAGATCG TCGGTTCAAA TCCGGCCCCC GCAACCA

Synthetic: No
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, EF-Tu

ProteinName: EF-Tu / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: nucleic-acid, Trp-tRNATrp

nucleic acidName: Trp-tRNATrp / Class: T-RNA / Structure: SINGLE STRANDED / Synthetic: No
Sequence:
AGGGGCGTAG TTCAATTGGT AGAGCACCGG TCTCCAAAAC CGGGTGTTGG GAGTTCGAGT CTCTCCGCCC CTGCCA
SourceSpecies: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.04 mg/mL
Buffer solution: HiFi (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)
pH: 7.5
VitrificationInstrument: FEI VITROBOT / Cryogen name: NITROGEN / Temperature: 80 K / Humidity: 90 % / Method: Blot for 6 seconds / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 58269 X (calibrated)
Astigmatism: Objective corrected at 100,000 times magnification
Imaging mode: BRIGHT FIELD / Defocus: 1200 - 4000 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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Image acquisition

Image acquisitionDetails: Automated data collection system AutoEMation (CCD mag. 100000x) TVIPS TemCam-F415

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 359223 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: back-projection / Software: Spider / CTF correction: Defocus groups, Wiener filter / Resolution: 8.25 Å / Resolution method: FSC at 0.5 cut-off (Gaussian mask)

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Atomic model buiding

Modeling #1Software: MDFF / Refinement protocol: flexible / Target criteria: RMSD, cross correlation / Refinement space: REAL / Details: Protocol: MD-based flexible fitting
Input PDB model: 2I2V

2i2v
PDB Unreleased entry

Modeling #2Software: MDFF / Refinement protocol: flexible / Target criteria: RMSD, cross correlation / Refinement space: REAL / Details: Protocol: MD-based flexible fitting
Input PDB model: 1OB2
Output model

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