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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 ribosome
  • RNA: deacylated tRNA
  • RNA: tRNA
  • RNA: tRNA
  • 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: Agirrezabala X / Fernandez IS / Kelley A / Gil Carton D / Ramakrishnan V / Valle M
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
  • Download
  • Surface view colored by height
  • Surface level: 0.175
  • Imaged by UCSF Chimera
  • Download
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.75 Å/pix.
x 210 pix.
= 367.5 Å		1.75 Å/pix.
x 210 pix.
= 367.5 Å		1.75 Å/pix.
x 210 pix.
= 367.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.75 Å
Density

Histogram

Histogram (log scale)
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 ribosome
  • RNA: deacylated tRNA
  • RNA: tRNA
  • RNA: tRNA
  • 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
Alignment procedureLegacy - Astigmatism: corrected at 100k
Specialist opticsEnergy filter - Name: in-column Omega filter / Energy filter - Lower energy threshold: 15.0 eV / Energy filter - Upper energy threshold: 20.0 eV
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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

Detailsparticles were selected by combining automated particle picking , multivariate data analysis and visual inspection
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

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Atomic model buiding 1

Initial modelPDB ID:

2wrn

SoftwareName: MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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Atomic model buiding 2

Initial modelPDB ID:

2wro

SoftwareName: MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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