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- EMDB-2170: Thermococcus kodakaraensis 70S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-2170
TitleThermococcus kodakaraensis 70S ribosome
Map dataThermococcus kodakaraensis 70S ribosome
Sample
  • Sample: Thermococcus kodakaraensis 70S ribosome
  • Complex: 70S ribosomeRibosome
Keywordsarchaea / ribosome 70S protein / RNA / kink-turn / protein synthesis / mass spectrometry
Biological speciesThermococcus kodakarensis (archaea)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 19.0 Å
AuthorsArmache J-P / Anger AM / Marquez V / Frankenberg S / Froehlich T / Villa E / Berninghausen O / Thomm M / Arnold GJ / Beckmann R / Wilson DN
CitationJournal: Nucleic Acids Res / Year: 2013
Title: Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution.
Authors: Jean-Paul Armache / Andreas M Anger / Viter Márquez / Sibylle Franckenberg / Thomas Fröhlich / Elizabeth Villa / Otto Berninghausen / Michael Thomm / Georg J Arnold / Roland Beckmann / Daniel N Wilson /
Abstract: In all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. Molecular models have been reported for complete bacterial 70S and eukaryotic 80S ribosomes; however, ...In all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. Molecular models have been reported for complete bacterial 70S and eukaryotic 80S ribosomes; however, only molecular models of large 50S subunits have been reported for archaea. Here, we present a complete molecular model for the Pyrococcus furiosus 70S ribosome based on a 6.6 Å cryo-electron microscopy map. Moreover, we have determined cryo-electron microscopy reconstructions of the Euryarchaeota Methanococcus igneus and Thermococcus kodakaraensis 70S ribosomes and Crenarchaeota Staphylothermus marinus 50S subunit. Examination of these structures reveals a surprising promiscuous behavior of archaeal ribosomal proteins: We observe intersubunit promiscuity of S24e and L8e (L7ae), the latter binding to the head of the small subunit, analogous to S12e in eukaryotes. Moreover, L8e and L14e exhibit intrasubunit promiscuity, being present in two copies per archaeal 50S subunit, with the additional binding site of L14e analogous to the related eukaryotic r-protein L27e. Collectively, these findings suggest insights into the evolution of eukaryotic ribosomal proteins through increased copy number and binding site promiscuity.
History
DepositionAug 9, 2012-
Header (metadata) releaseOct 3, 2012-
Map releaseFeb 13, 2013-
UpdateFeb 13, 2013-
Current statusFeb 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2170.png

Downloads & links

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Map

FileDownload / File: emd_2170.map.gz / Format: CCP4 / Size: 50.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThermococcus kodakaraensis 70S ribosome
Voxel size
XYZ
EMDB info.3.313.313.31
CCP4 map header3.313.313.31
EM Navigator Movie #11.241.241.24
Density
Contour LevelBy EMDB: 0.001 / Movie #1: 0.0006
Minimum - Maximum0.0 - 0.002648
Average (Standard dev.)0.0001853 (±0.00041397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-126-101-165
Dimensions229225263
Spacing225229263
CellA: 757.99 Å / B: 744.75 Å / C: 870.52997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.313.313.31
M x/y/z229225263
origin x/y/z0.0000.0000.000
length x/y/z757.990744.750870.530
α/β/γ90.00090.00090.000
start NX/NY/NZ-126-101-165
NX/NY/NZ229225263
MAP C/R/S213
start NC/NR/NS-101-126-165
NC/NR/NS225229263
D min/max/mean0.0000.0030.000

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Supplemental data

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Sample components

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Entire : Thermococcus kodakaraensis 70S ribosome

EntireName: Thermococcus kodakaraensis 70S ribosome
Components
  • Sample: Thermococcus kodakaraensis 70S ribosome
  • Complex: 70S ribosomeRibosome

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Supramolecule #1000: Thermococcus kodakaraensis 70S ribosome

SupramoleculeName: Thermococcus kodakaraensis 70S ribosome / type: sample / ID: 1000 / Oligomeric state: One ribosome / Number unique components: 1
Molecular weightExperimental: 2.1 MDa / Theoretical: 2.1 MDa

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Supramolecule #1: 70S ribosome

SupramoleculeName: 70S ribosome / type: complex / ID: 1 / Name.synonym: 70S ribosome / Recombinant expression: No
Ribosome-details: ribosome-prokaryote: LSU 50S, LSU RNA 23S, LSU RNA 5S, SSU 30S, PSR16s, ALL
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightExperimental: 2.1 MDa / Theoretical: 2.1 MDa

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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

BufferpH: 7.5
StainingType: NEGATIVE
Details: 20 mM Hepes pH 7.5, 10 mM Mg(OAc)2, 30 mM NH4OAc, 4 mM beta-Mercaptoethanol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I / Details: Vitrification instrument: Vitrobot
Method: Blot for 10 seconds before plunging, use 2 layers of filter paper

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 90000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 90000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateAug 9, 2008
Image recordingCategory: FILM / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Scanner: OTHER / Number real images: 99 / Average electron dose: 20 e/Å2 / Details: Eagle 4k CCD

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Image processing

CTF correctionDetails: Wiener filter on 3D volumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 10431

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Atomic model buiding 1

Initial modelPDB ID:

3cc2

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid-body fit into the density using UCSF Chimera built-in "Fit in Map". Rigid-body fit into the density using UCSF Chimera built-in "Fit in Map"
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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