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- EMDB-2171: Staphylothermus marinus 50S ribosomal subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-2171
TitleStaphylothermus marinus 50S ribosomal subunit
Map dataStaphylothermus marinus 50S ribosomal subunit
Sample
  • Sample: Staphylothermus marinus 50S ribosomal subunit
  • Complex: Staphylothermus marinus 50S ribosomal subunit
Keywordsarchaea / ribosome 50S protein / RNA / kink-turn / protein synthesis / mass spectrometry
Biological speciesStaphylothermus marinus (archaea)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 24.0 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: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2171.png

Downloads & links

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Map

FileDownload / File: emd_2171.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStaphylothermus marinus 50S ribosomal subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
3.31 Å/pix.
x 368 pix.
= 1218.08 Å		3.31 Å/pix.
x 368 pix.
= 1218.08 Å		3.31 Å/pix.
x 368 pix.
= 1218.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.3.313.313.31
CCP4 map header3.313.313.31
EM Navigator Movie #11.241.241.24
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 3.61 / Movie #1: 1
Minimum - Maximum-2.46412158 - 5.88103676
Average (Standard dev.)0.0237666 (±0.65059769)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 1218.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.313.313.31
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z1218.0801218.0801218.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S213
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-2.4645.8810.024

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Supplemental data

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Sample components

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Entire : Staphylothermus marinus 50S ribosomal subunit

EntireName: Staphylothermus marinus 50S ribosomal subunit
Components
  • Sample: Staphylothermus marinus 50S ribosomal subunit
  • Complex: Staphylothermus marinus 50S ribosomal subunit

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Supramolecule #1000: Staphylothermus marinus 50S ribosomal subunit

SupramoleculeName: Staphylothermus marinus 50S ribosomal subunit / type: sample / ID: 1000 / Oligomeric state: One ribosomal subunit / Number unique components: 1
Molecular weightExperimental: 1.5 MDa / Theoretical: 1.5 MDa

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Supramolecule #1: Staphylothermus marinus 50S ribosomal subunit

SupramoleculeName: Staphylothermus marinus 50S ribosomal subunit / type: complex / ID: 1 / Name.synonym: 50S ribosomal subunit / Recombinant expression: No
Ribosome-details: ribosome-prokaryote: LSU 50S, LSU RNA 23S, LSU RNA 5S
Source (natural)Organism: Staphylothermus marinus (archaea)
Molecular weightExperimental: 1.5 MDa / Theoretical: 1.5 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 III / 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
DateSep 6, 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: Data collected on CCD
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 90000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 90000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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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: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 11142

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Atomic model buiding 1

Initial modelPDB ID:

3cc2

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

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