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- EMDB-1019: The Escherichia coli large ribosomal subunit at 7.5 A resolution. -

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Basic information

Entry
Database: EMDB / ID: EMD-1019
TitleThe Escherichia coli large ribosomal subunit at 7.5 A resolution.
Map dataThe Escherichia coli large ribosomal subunit at 7.5 A resolution.
Sample
  • Sample: 50S E.coli ribosomal subunit
  • Complex: 50S ribosomal subunit
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsMatadeen R
CitationJournal: Structure / Year: 1999
Title: The Escherichia coli large ribosomal subunit at 7.5 A resolution.
Authors: R Matadeen / A Patwardhan / B Gowen / E V Orlova / T Pape / M Cuff / F Mueller / R Brimacombe / M van Heel /
Abstract: BACKGROUND: In recent years, the three-dimensional structure of the ribosome has been visualised in different functional states by single-particle cryo-electron microscopy (cryo-EM) at 13-25 A ...BACKGROUND: In recent years, the three-dimensional structure of the ribosome has been visualised in different functional states by single-particle cryo-electron microscopy (cryo-EM) at 13-25 A resolution. Even more recently, X-ray crystallography has achieved resolution levels better than 10 A for the ribosomal structures of thermophilic and halophilic organisms. We present here the 7.5 A solution structure of the 50S large subunit of the Escherichia coli ribosome, as determined by cryo-EM and angular reconstitution.
RESULTS: The reconstruction reveals a host of new details including the long alpha helix connecting the N- and C-terminal domains of the L9 protein, which is found wrapped like a collar around the ...RESULTS: The reconstruction reveals a host of new details including the long alpha helix connecting the N- and C-terminal domains of the L9 protein, which is found wrapped like a collar around the base of the L1 stalk. A second L7/L12 dimer is now visible below the classical L7/L12 'stalk', thus revealing the position of the entire L8 complex. Extensive conformational changes occur in the 50S subunit upon 30S binding; for example, the L9 protein moves by some 50 A. Various rRNA stem-loops are found to be involved in subunit binding: helix h38, located in the A-site finger; h69, on the rim of the peptidyl transferase centre cleft; and h34, in the principal interface protrusion.
CONCLUSIONS: Single-particle cryo-EM is rapidly evolving towards the resolution levels required for the direct atomic interpretation of the structure of the ribosome. Structural details such as the ...CONCLUSIONS: Single-particle cryo-EM is rapidly evolving towards the resolution levels required for the direct atomic interpretation of the structure of the ribosome. Structural details such as the minor and major grooves in rRNA double helices and alpha helices of the ribosomal proteins can already be visualised directly in cryo-EM reconstructions of ribosomes frozen in different functional states.
History
Header (metadata) releaseJun 5, 2002-
DepositionNov 28, 2002-
Map releaseJan 6, 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: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1019.gif

Downloads & links

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Map

FileDownload / File: emd_1019.map.gz / Format: CCP4 / Size: 20.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe Escherichia coli large ribosomal subunit at 7.5 A resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 146 pix.
= 286.16 Å		1.96 Å/pix.
x 192 pix.
= 376.32 Å		1.96 Å/pix.
x 192 pix.
= 376.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel size
XYZ
EMDB info.1.961.961.96
CCP4 map header1.961.961.96
EM Navigator Movie #11.761.761.76
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0584 / Movie #1: 0.05
Minimum - Maximum-0.370668 - 0.393129
Average (Standard dev.)0.00348208 (±0.0374738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192146
Spacing192192146
CellA: 376.32 Å / B: 376.32 Å / C: 286.16 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.961.961.96
M x/y/z192192146
origin x/y/z0.0000.0000.000
length x/y/z376.320376.320286.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192146
D min/max/mean-0.3710.3930.003

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Supplemental data

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Sample components

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Entire : 50S E.coli ribosomal subunit

EntireName: 50S E.coli ribosomal subunit
Components
  • Sample: 50S E.coli ribosomal subunit
  • Complex: 50S ribosomal subunit

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Supramolecule #1000: 50S E.coli ribosomal subunit

SupramoleculeName: 50S E.coli ribosomal subunit / type: sample / ID: 1000 / Oligomeric state: single entity / Number unique components: 1
Molecular weightExperimental: 1.5 MDa / Theoretical: 1.5 MDa / Method: Sedimentation

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Supramolecule #1: 50S ribosomal subunit

SupramoleculeName: 50S ribosomal subunit / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightExperimental: 1.5 MDa / Theoretical: 1.5 MDa

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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

Concentration1 mg/mL
BufferpH: 7.4 / Details: 20mM HEPES-KOH 6 mM MgCl2, 150 mM NH4Cl
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: in-house freeze plunger / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/UT
TemperatureAverage: 96 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PATCHWORK DENSITOMETER / Digitization - Sampling interval: 5 µm / Number real images: 7 / Average electron dose: 10 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 38000
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: Imagic / Number images used: 16000
Final two d classificationNumber classes: 1000

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Atomic model buiding 1

SoftwareName: ESSENS

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