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- EMDB-2373: ribosome-RelA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-2373
Titleribosome-RelA complex
Map datareconstruction of ribosome-RelA complex
Sample
  • Sample: 70S-RelA complex
  • Complex: 70S ribosomeRibosome
  • RNA: deacylated tRNA
  • RNA: tRNATransfer RNA
  • RNA: tRNATransfer RNA
  • Protein or peptide: RelA
Keywordsribosome / RelA / stringent response
Biological speciesThermus thermophilus (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.5 Å
AuthorsAgirrezabala X / Fernandez I / Kelley A / Gil-Carton D / Ramakrishnan V / Valle M
CitationJournal: EMBO Rep / Year: 2013
Title: The ribosome triggers the stringent response by RelA via a highly distorted tRNA.
Authors: Xabier Agirrezabala / Israel S Fernández / Ann C Kelley / David Gil Cartón / Venki Ramakrishnan / Mikel Valle /
Abstract: The bacterial stringent response links nutrient starvation with the transcriptional control of genes. This process is initiated by the stringent factor RelA, which senses the presence of deacylated ...The bacterial stringent response links nutrient starvation with the transcriptional control of genes. This process is initiated by the stringent factor RelA, which senses the presence of deacylated tRNA in the ribosome as a symptom of amino-acid starvation to synthesize the alarmone (p)ppGpp. Here we report a cryo-EM study of RelA bound to ribosomes bearing cognate, deacylated tRNA in the A-site. The data show that RelA on the ribosome stabilizes an unusual distorted form of the tRNA, with the acceptor arm making contact with RelA and far from its normal location in the peptidyl transferase centre.
History
DepositionMay 14, 2013-
Header (metadata) releaseMay 29, 2013-
Map releaseJul 31, 2013-
UpdateSep 11, 2013-
Current statusSep 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.175
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.175
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2373-4.tif

Downloads & links

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Map

FileDownload / File: emd_2373.map.gz / Format: CCP4 / Size: 34.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of ribosome-RelA complex
Voxel sizeX=Y=Z: 1.75 Å
Density
Contour LevelBy AUTHOR: 0.175 / Movie #1: 0.175
Minimum - Maximum-0.22494394 - 1.17451715
Average (Standard dev.)0.0393284 (±0.15456907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 367.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.751.751.75
M x/y/z210210210
origin x/y/z0.0000.0000.000
length x/y/z367.500367.500367.500
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.2251.1750.039

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Supplemental data

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Sample components

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Entire : 70S-RelA complex

EntireName: 70S-RelA complex
Components
  • Sample: 70S-RelA complex
  • Complex: 70S ribosomeRibosome
  • RNA: deacylated tRNA
  • RNA: tRNATransfer RNA
  • RNA: tRNATransfer RNA
  • Protein or peptide: RelA

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Supramolecule #1000: 70S-RelA complex

SupramoleculeName: 70S-RelA complex / type: sample / ID: 1000 / Number unique components: 5
Molecular weightTheoretical: 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: ALL
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 2.5 MDa

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Macromolecule #1: deacylated tRNA

MacromoleculeName: deacylated tRNA / type: rna / ID: 1 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Thermus thermophilus (bacteria)

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Macromolecule #2: tRNA

MacromoleculeName: tRNA / type: rna / ID: 2 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Thermus thermophilus (bacteria)

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Macromolecule #3: tRNA

MacromoleculeName: tRNA / type: rna / ID: 3 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Thermus thermophilus (bacteria)

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Macromolecule #4: RelA

MacromoleculeName: RelA / type: protein_or_peptide / ID: 4 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.45
Details: 5mM Hepes-KOH pH 7.45, 50mM KCl, 10mM NH4Cl, 10mM Mg-acetate, 5mM beta-mercapto-ethanol
StainingType: NEGATIVE / Details: cryo
GridDetails: Quantifoil grids (2/4) with thin carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Specialist opticsEnergy filter - Name: in-column Omega filter / Energy filter - Lower energy threshold: 15.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: corrected at 100k
DateJan 15, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 425 / Average electron dose: 10 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: defocus groups
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP, SPIDER / Number images used: 28791
Detailsparticles were selected by combining automated particle picking , multivariate data analysis and visual inspection

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Atomic model buiding 1

Initial modelPDB ID:

2wrn
PDB Unreleased entry

SoftwareName: MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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Atomic model buiding 2

Initial modelPDB ID:

2wro
PDB Unreleased entry

SoftwareName: MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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