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- EMDB-1212: Hrr25-dependent phosphorylation state regulates organization of t... -

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Basic information

Entry
Database: EMDB / ID: 1212
TitleHrr25-dependent phosphorylation state regulates organization of the pre-40S subunit.
Map datamap of 40S ribosome
Sample40S Ribosome:
ribosome-eukaryote
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 32 Å resolution
AuthorsSchafer T / Maco B / Petfalski E / Tollervey D / Bottcher B / Aebi U / Hurt E
CitationJournal: Nature / Year: 2006
Title: Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit.
Authors: Thorsten Schäfer / Bohumil Maco / Elisabeth Petfalski / David Tollervey / Bettina Böttcher / Ueli Aebi / Ed Hurt
DateDeposition: Mar 29, 2006 / Header (metadata) release: Apr 3, 2006 / Map release: Jun 1, 2006 / Last update: Oct 17, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1212.map.gz (map file in CCP4 format, 2001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
5.72 Å/pix.
= 457.6 Å
80 pix
5.72 Å/pix.
= 457.6 Å
80 pix
5.72 Å/pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.72 Å
Density
Contour Level:0.211, 0.3 (movie #1):
Minimum - Maximum-1.08288 - 2.18498
Average (Standard dev.)0.00655999 (0.135631)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin-40-40-40
Limit393939
Spacing808080
CellA=B=C: 457.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.725.725.72
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z457.600457.600457.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-1.0832.1850.007

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Supplemental data

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Sample components

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Entire 40S Ribosome

EntireName: 40S Ribosome / Details: sample was purified from S. cervisiae / Oligomeric State: monomer / Number of components: 1

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Component #1: ribosome-eukaryote, 40S-ribosome

Ribosome-eukaryoteName: 40S-ribosome / Eukaryote: SSU 40S / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 50mM Tris-HCl, 100mM NaCl, 10mM MgCl2, 0.5mM DTT
pH: 7.5
Support film400 mesh copper rhodium grids (Maxtaform)
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 90 % / Method: Blot for 15 s with Whatman No 1
Details: Vitrification instrument: Plunger with environmental chamber

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Astigmatism: bjective lens astigmatism was corrected at / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3200 - 5000 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 94 K
CameraDetector: GENERIC CCD

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Image acquisition

Image acquisitionNumber of digital images: 69 / Sampling size: 14 microns / Bit depth: 12

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 236 / Number of projections: 4827
Details: 236 out of 400 classes were used for final reconstruction
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: weighted back projection / Software: IMAGIC 5 / CTF correction: Each Particle / Resolution: 32 Å / Resolution method: FSC 0.5 / Euler angles: IMAGIC
Details: reconstructions were calculated from half of the class averages. Euler angles of class averages were determined by projection matching

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