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- EMDB-1924: Ribosome Assembly Factors Prevent Premature Translation Initiatio... -

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Basic information

Entry
Database: EMDB / ID: 1924
TitleRibosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates
Keywordspre-40S / 40S intermediate / Ltv1 deletion
SampleS. cerevisiae pre-40S ribosomal particle with Ltv1 deletion
SourceSaccharomyces cerevisiae / yeast / Bakers' yeast / サッカロミセス・セレビシエ /
Map dataSurface rendered Ltv1 deletion map
Methodsingle particle reconstruction, at 20 Å resolution
AuthorsStrunk BS / Loucks CR / Su M / Vashisth H / Cheng S / Schilling J / BrooksIII CL / Karbstein K / Skiniotis G
CitationScience, 2011, 333, 1449-1453

Science, 2011, 333, 1449-1453 StrPapers
Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates.
Bethany S Strunk / Cherisse R Loucks / Min Su / Harish Vashisth / Shanshan Cheng / Justin Schilling / Charles L Brooks / Katrin Karbstein / Georgios Skiniotis

DateDeposition: Jul 5, 2011 / Header (metadata) release: Nov 4, 2011 / Map release: Nov 4, 2011 / Last update: Jul 5, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_1924.map.gz (map file in CCP4 format, 16001 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.24 Å/pix.
= 358.4 Å
160 pix
2.24 Å/pix.
= 358.4 Å
160 pix
2.24 Å/pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.24 Å
Density
Contour Level:0.3 (by author), 0.5 (movie #1):
Minimum - Maximum-2.1019 - 3.94117
Average (Standard dev.)0.0028384 (0.359594)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin000
Limit159159159
Spacing160160160
CellA=B=C: 358.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.242.242.24
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-2.1023.9410.003

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Supplemental data

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Sample components

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Entire S. cerevisiae pre-40S ribosomal particle with Ltv1 deletion

EntireName: S. cerevisiae pre-40S ribosomal particle with Ltv1 deletion
Details: Monodisperse / Number of components: 1
MassTheoretical: 1.4 MDa

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

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

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1.5 mg/ml
Buffer solution: 50mM Tris-Cl, 100mM NaCl, 10mM MgCl2, 0.075% NP40, 1mM imidazole, 2mM EGTA, 10 mM BME
pH: 7.5
Support filmQuantifoil
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 85 K / Humidity: 100 % / Method: Blot for 2 seconds before plunging / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 16 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 66964 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4000 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: OTHER / Temperature: 89 K ( 89 - 89 K)
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 350 / Sampling size: 2.24 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 10235 / Details: Manual particle selection / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Euler angles: EMAN convention / Software: EMAN / CTF correction: Each micrograph / Details: Final map was filtered to 20A resolution / Resolution: 20 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: NAMD / Refinement protocol: flexible / Target criteria: CC / Refinement space: REAL / Details: Protocol: MDFF
Input PDB model: 3O2Z

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