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- EMDB-1004: Ribosome interactions of aminoacyl-tRNA and elongation factor Tu ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1004
TitleRibosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
Map data70S ribosome stalled by the antibiotic kirromycin
Sample
  • Sample: Kirromycin stalled 70S Ribosome from E.coli
  • Complex: 70S RibosomeRibosome
  • Ligand: EF-Tu, tRNA, GTP
  • RNA: formyl-methionyl tRNA
Function / homology
Function and homology information


misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic large ribosomal subunit ...misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / positive regulation of RNA splicing / maintenance of translational fidelity / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / GTPase activity / GTP binding / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / 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 / Elongation factor Tu domain 2 ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / 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 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / 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/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, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal protein S13, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13-like, H2TH / Ribosomal protein S13 signature. / Ribosomal protein S13 family profile. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS13 / Elongation factor Tu / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsStark H / Rodnina MV / Wieden HJ / Zemlin F / Wintermeyer W / van Heel M
CitationJournal: Nat Struct Biol / Year: 2002
Title: Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
Authors: Holger Stark / Marina V Rodnina / Hans-Joachim Wieden / Friedrich Zemlin / Wolfgang Wintermeyer / Marin van Heel /
Abstract: The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional ...The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional reconstruction determined by cryo-electron microscopy of the kirromycin-stalled codon-recognition complex. The structure of the ternary complex is distorted by binding of the tRNA anticodon arm in the decoding center. The aa-tRNA interacts with 16S rRNA, helix 69 of 23S rRNA and proteins S12 and L11, while the sarcin-ricin loop of 23S rRNA contacts domain 1 of EF-Tu near the nucleotide-binding pocket. These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation.
History
DepositionAug 27, 2002-
Header (metadata) releaseAug 29, 2002-
Map releaseAug 29, 2003-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1004.gif

Downloads & links

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Map

FileDownload / File: emd_1004.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation70S ribosome stalled by the antibiotic kirromycin
Voxel sizeX=Y=Z: 2.25 Å
Density
Contour Level1: 0.0411 / Movie #1: 0.02
Minimum - Maximum-0.480909 - 0.774331
Average (Standard dev.)0.00151584 (±0.0461972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 360 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.252.252.25
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z360.000360.000360.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.4810.7740.002

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Supplemental data

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Sample components

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Entire : Kirromycin stalled 70S Ribosome from E.coli

EntireName: Kirromycin stalled 70S Ribosome from E.coli
Components
  • Sample: Kirromycin stalled 70S Ribosome from E.coli
  • Complex: 70S RibosomeRibosome
  • Ligand: EF-Tu, tRNA, GTP
  • RNA: formyl-methionyl tRNA

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Supramolecule #1000: Kirromycin stalled 70S Ribosome from E.coli

SupramoleculeName: Kirromycin stalled 70S Ribosome from E.coli / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 3
Molecular weightExperimental: 2.5 MDa / Theoretical: 2.5 MDa

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Supramolecule #1: 70S Ribosome

SupramoleculeName: 70S Ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 2.5 MDa

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Macromolecule #1: EF-Tu, tRNA, GTP

MacromoleculeName: EF-Tu, tRNA, GTP / type: ligand / ID: 1 / Name.synonym: Ternary Complex / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 64 KDa

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Macromolecule #2: formyl-methionyl tRNA

MacromoleculeName: formyl-methionyl tRNA / type: rna / ID: 2 / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.07 mg/mL
BufferpH: 7.5
Details: 50mM Tris-HCl, 70mM NH4Cl, 30mM KCl, 7mM MgCl2, 1mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 40 %

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/SOPHIE
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.35 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder: side entry / Specimen holder model: HOME BUILD
TemperatureMin: 4.2 K / Max: 4.2 K / Average: 4.2 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PATCHWORK DENSITOMETER / Digitization - Sampling interval: 13.2 µm / Average electron dose: 15 e/Å2 / Od range: 1.3 / Bits/pixel: 8

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Image processing

CTF correctionDetails: phase flip
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: Imagic / Number images used: 24000

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Atomic model buiding 1

SoftwareName: Situs and Amira
DetailsProtocol: rigid body. The domains of EF-Tu were fitted seperately by visual docking using O and Swiss PDB viewer
RefinementProtocol: RIGID BODY FIT
Output model

PDB-1mj1:
FITTING THE TERNARY COMPLEX OF EF-Tu/tRNA/GTP AND RIBOSOMAL PROTEINS INTO A 13 A CRYO-EM MAP OF THE COLI 70S RIBOSOME

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