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- EMDB-1329: Reconfiguration of yeast 40S ribosomal subunit domains by the tra... -

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Basic information

Entry
Database: EMDB / ID: EMD-1329
TitleReconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
Map dataReconstruction of subclass I of a 31756 image dataset for the 43S translation preinitiation complex.
Sample
  • Sample: Eukaryotic translation preinitiation complex 43S
  • Complex: Small subunit
  • RNA: tRNA
  • Protein or peptide: eukaryotic translation initiation factor 2
  • Protein or peptide: eukaryotic translation initiation factor 3
  • Protein or peptide: eukaryotic translation initiation factor 1
  • Protein or peptide: eukaryotic translation initiation factor 1A
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 30.0 Å
AuthorsGilbert RJC / Gordiyenko Y / von der Haar T
CitationJournal: Proc Natl Acad Sci U S A / Year: 2007
Title: Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
Authors: 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 /
Abstract: In the process of protein synthesis, the small (40S) subunit of the eukaryotic ribosome is recruited to the capped 5' end of the mRNA, from which point it scans along the 5' untranslated region in ...In the process of protein synthesis, the small (40S) subunit of the eukaryotic ribosome is recruited to the capped 5' end of the mRNA, from which point it scans along the 5' untranslated region in search of a start codon. However, the 40S subunit alone is not capable of functional association with cellular mRNA species; it has to be prepared for the recruitment and scanning steps by interactions with a group of eukaryotic initiation factors (eIFs). In budding yeast, an important subset of these factors (1, 2, 3, and 5) can form a multifactor complex (MFC). Here, we describe cryo-EM reconstructions of the 40S subunit, of the MFC, and of 40S complexes with MFC factors plus eIF1A. These studies reveal the positioning of the core MFC on the 40S subunit, and show how eIF-binding induces mobility in the head and platform and reconfigures the head-platform-body relationship. This is expected to increase the accessibility of the mRNA channel, thus enabling the 40S subunit to convert to a recruitment-competent state.
History
DepositionMar 6, 2007-
Header (metadata) releaseMar 6, 2007-
Map releaseApr 6, 2007-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.51744696
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.51744696
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1329.gif

Downloads & links

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Map

FileDownload / File: emd_1329.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of subclass I of a 31756 image dataset for the 43S translation preinitiation complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
3.33 Å/pix.
x 128 pix.
= 426.24 Å		3.33 Å/pix.
x 128 pix.
= 426.24 Å		3.33 Å/pix.
x 128 pix.
= 426.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.33 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 9.880000000000001 / Movie #1: 4.517447
Minimum - Maximum-42.004600000000003 - 90.063999999999993
Average (Standard dev.)0.591695 (±6.18805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 426.24 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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-42.00590.0640.592

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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
Components
  • Sample: Eukaryotic translation preinitiation complex 43S
  • Complex: Small subunit
  • RNA: tRNA
  • Protein or peptide: eukaryotic translation initiation factor 2
  • Protein or peptide: eukaryotic translation initiation factor 3
  • Protein or peptide: eukaryotic translation initiation factor 1
  • Protein or peptide: eukaryotic translation initiation factor 1A

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Supramolecule #1000: Eukaryotic translation preinitiation complex 43S

SupramoleculeName: Eukaryotic translation preinitiation complex 43S / type: sample / ID: 1000 / Oligomeric state: 40S-Met-tRNA-eIF2-GMP-PNP-eIF3-eIF1-eIF1A / Number unique components: 6
Molecular weightTheoretical: 1.941 MDa

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Supramolecule #1: Small subunit

SupramoleculeName: Small subunit / type: complex / ID: 1 / Name.synonym: 40S / Details: S. cerevisiae / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
Molecular weightExperimental: 1.4 MDa / Theoretical: 1.4 MDa

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Macromolecule #1: tRNA

MacromoleculeName: tRNA / type: rna / ID: 1 / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 23 KDa / Theoretical: 23 KDa

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Macromolecule #2: eukaryotic translation initiation factor 2

MacromoleculeName: eukaryotic translation initiation factor 2 / type: protein_or_peptide / ID: 2 / Name.synonym: eIF2 / Number of copies: 1 / Oligomeric state: heterotrimer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Cytosol
Molecular weightExperimental: 124 KDa / Theoretical: 124 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #3: eukaryotic translation initiation factor 3

MacromoleculeName: eukaryotic translation initiation factor 3 / type: protein_or_peptide / ID: 3 / Name.synonym: eIF3 / Number of copies: 1 / Oligomeric state: Heteropentamer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Cytosol
Molecular weightExperimental: 362 KDa / Theoretical: 362 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #4: eukaryotic translation initiation factor 1

MacromoleculeName: eukaryotic translation initiation factor 1 / type: protein_or_peptide / ID: 4 / Name.synonym: eIF1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Cytosol
Molecular weightExperimental: 12 KDa / Theoretical: 12 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #5: eukaryotic translation initiation factor 1A

MacromoleculeName: eukaryotic translation initiation factor 1A / type: protein_or_peptide / ID: 5 / Name.synonym: eIF1A / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Cytosol
Molecular weightExperimental: 17 KDa / Theoretical: 17 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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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

BufferpH: 7.4
Details: 38mM HEPES, 135mM KAc, 3.25mM MgAc2, 5mM beta-mercaptoethanol, 10uM GMP-PNP
GridDetails: 300 mesh copper grid with lacey carbon film
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home-made plunger
Method: Blot with Whatman number 1 paper for 1-2 seconds prior to plunging.

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Astigmatism corrected at 100,000 x
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 8.33 µm / Number real images: 70 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 11.685 µm / Nominal defocus min: 2.055 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected manually.
CTF correctionDetails: Per micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, EMAN, FREALIGN, SPIDER, GAP
Details: Final maps were computed from CTF-corrected (by phase flipping) images, and scaled in Fourier space to a scattering model of the structure.
Number images used: 6864
Final angle assignmentDetails: SPIDER Euler angle convention

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Atomic model buiding 1

SoftwareName: GAP
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Real space CC and R-factor

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