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- EMDB-1327: Reconfiguration of yeast 40S ribosomal subunit domains by the tra... -

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Basic information

Entry
Database: EMDB / ID: 1327
TitleReconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
SampleEukaryotic translation preinitiation complex 43S
SourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Map dataReconstruction of the 43S preinitiation complex from S. cerevisiae.
Methodsingle particle reconstruction, at 20 A resolution
AuthorsGilbert RJC / Gordiyenko Y / von der Haar T / Sonnen AF-P / Hoffman GW / Nardelli M / Stuart DI / McCarthy JEG
CitationProc. Natl. Acad. Sci. U.S.A., 2007, 104, 5788-5793

Proc. Natl. Acad. Sci. U.S.A., 2007, 104, 5788-5793 StrPapers
Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
Robert J C Gilbert / Yulya Gordiyenko / Tobias von der Haar / Andreas F-P Sonnen / Gregor Hofmann / Maria Nardelli / David I Stuart / John E G McCarthy

DateDeposition: Mar 6, 2007 / Header (metadata) release: Mar 6, 2007 / Map release: Apr 6, 2007 / Last update: Mar 6, 2007

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 22.408501399
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 22.408501399
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1327.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices
Size
Brightness
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Others
AxesY (Sec.)X (Row.)Z (Col.)
128 pix
3.33 A/pix
= 426.24 A
128 pix
3.33 A/pix
= 426.24 A
128 pix
3.33 A/pix
= 426.24 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.33 A
Density
Contour Level:21.7, 22.4085014 (movie #1):
Minimum - Maximum-97.4 - 200
Average (Standard dev.)1.93102 (13.2256)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
CellA=B=C: 426.24 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z3.333.333.33
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z426.240426.240426.240
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S312
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-97.400200.0001.931

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Supplemental data

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Sample components

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Entire Eukaryotic translation preinitiation complex 43S

EntireName: Eukaryotic translation preinitiation complex 43S / Oligomeric State: 40S-Met-tRNA-eIF2-GMP-PNP-eIF3-eIF1-eIF1A / Number of components: 6
MassTheoretical: 1.941 MDa

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Component #1: ribosome-eukaryote, Small subunit

Ribosome-eukaryoteName: Small subunit / a.k.a: 40S / Details: S. cerevisiae / Eukaryote: SSU 40S / Recombinant expression: No
MassTheoretical: 1.4 MDa / Experimental: 1.4 MDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /

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Component #2: nucleic-acid, tRNA

Nucleic-acidName: tRNA / Class: T-RNA / Structure: DOUBLE HELIX / Synthetic: No
MassTheoretical: 23 kDa / Experimental: 23 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /

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Component #3: protein, eukaryotic translation initiation factor 2

ProteinName: eukaryotic translation initiation factor 2 / a.k.a: eIF2 / Oligomeric Details: heterotrimer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 124 kDa / Experimental: 124 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (natural)Location in cell: Cytosol

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Component #4: protein, eukaryotic translation initiation factor 3

ProteinName: eukaryotic translation initiation factor 3 / a.k.a: eIF3 / Oligomeric Details: Heteropentamer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 362 kDa / Experimental: 362 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (natural)Location in cell: Cytosol

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Component #5: protein, eukaryotic translation initiation factor 1

ProteinName: eukaryotic translation initiation factor 1 / a.k.a: eIF1 / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 12 kDa / Experimental: 12 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (natural)Location in cell: Cytosol

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Component #6: protein, eukaryotic translation initiation factor 1A

ProteinName: eukaryotic translation initiation factor 1A / a.k.a: eIF1A / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 17 kDa / Experimental: 17 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (natural)Location in cell: Cytosol

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 38mM HEPES, 135mM KAc, 3.25mM MgAc2, 5mM beta-mercaptoethanol, 10uM GMP-PNP
pH: 7.4
Support film300 mesh copper grid with lacey carbon film
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Method: Blot with Whatman number 1 paper for 1-2 seconds prior to plunging.
Details: Vitrification instrument: Home-made plunger

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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: Astigmatism corrected at 100,000 x / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2055 - 11685 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 100 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 70 / Scanner: OTHER / Sampling size: 8.33 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 27101 / Details: The particles were selected manually. / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Single particle / Software: IMAGIC, EMAN, FREALIGN, SPIDER, GAP / CTF correction: Per micrograph / Resolution: 20 A / Resolution method: FSC 0.5 / Euler angles: SPIDER Euler angle convention
Details: Final maps were computed from CTF-corrected (by phase flipping) images, and scaled in Fourier space to a scattering model of the structure.

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Atomic model buiding

Modeling #1Software: GAP / Refinement protocol: rigid body / Target criteria: Real space CC and R-factor / Refinement space: REAL / Details: Protocol: Rigid body

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