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- EMDB-2858: Cryo-EM structure of yeast 80S ribosome calculated on Amazon's el... -

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Basic information

Entry
Database: EMDB / ID: EMD-2858
TitleCryo-EM structure of yeast 80S ribosome calculated on Amazon's elastic cloud computing network
Map data80S yeast ribosome reconstructed using Relion from published dataset EMPIAR ID 10002.
Sample
  • Sample: 80S yeast ribosome
  • Complex: 80S ribosome
KeywordsRibosome / yeast / Relion / Amazon
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsCianfrocco MA / Leschziner AE
CitationJournal: Elife / Year: 2015
Title: Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud.
Authors: Michael A Cianfrocco / Andres E Leschziner /
Abstract: The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high- ...The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available 'off-the-shelf' computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16-480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM.
History
DepositionJan 22, 2015-
Header (metadata) releaseApr 1, 2015-
Map releaseFeb 3, 2016-
UpdateFeb 3, 2016-
Current statusFeb 3, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.215
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.215
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2858.png

Downloads & links

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Map

FileDownload / File: emd_2858.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation80S yeast ribosome reconstructed using Relion from published dataset EMPIAR ID 10002.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 240 pix.
= 424.8 Å		1.77 Å/pix.
x 240 pix.
= 424.8 Å		1.77 Å/pix.
x 240 pix.
= 424.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.215 / Movie #1: 0.215
Minimum - Maximum-0.43449956 - 0.87536299
Average (Standard dev.)0.00420341 (±0.06088743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 424.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z424.800424.800424.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.4340.8750.004

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Supplemental data

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Sample components

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Entire : 80S yeast ribosome

EntireName: 80S yeast ribosome
Components
  • Sample: 80S yeast ribosome
  • Complex: 80S ribosome

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Supramolecule #1000: 80S yeast ribosome

SupramoleculeName: 80S yeast ribosome / type: sample / ID: 1000
Details: Micrographs were downloaded from EMPIAR dataset 10002, associated with the publication Bai et al. eLife (2013)
Oligomeric state: ribosome-eukaryote / Number unique components: 1
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 MDa

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1
Details: Micrographs were downloaded from EMPAIR database 10002, associated with Bai et al. eLife (2013)
Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers' yeast
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 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

Concentration0.3 mg/mL
BufferpH: 7.45
Details: 3mM Hepes-KOH, 6.6 mM Tris-acetate pH 7.2, 3 mM NH4Cl, 6.6 mM NH4-acetate, 48 mM K-acetate, 4 mM Mg-acetate, 2.4 mM DTT
GridDetails: Quantifoil grids (2/2) with 3 nm thin carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK II
Details: Micrographs were downloaded from EMPIAR database 10002, associated with Bai et al. eLife (2013)
Method: Blot 2.5 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification
DetailsMicrographs were downloaded from EMPIAR 10002
DateJul 15, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 200 / Average electron dose: 16 e/Å2
Details: Every image is the average of sixteen frames recorded by the direct electron detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 79096 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.44 µm / Nominal defocus min: 1.191 µm
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsParticles were extracted and processed using Relion
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 32533
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3u5b
PDB Unreleased entry

SoftwareName: Chimera
DetailsEach PDB model was docked using "Fit in map" in Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

3u5c
PDB Unreleased entry

SoftwareName: Chimera
DetailsEach PDB model was docked using "Fit in map" in Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 3

Initial modelPDB ID:

3u5d
PDB Unreleased entry

SoftwareName: Chimera
DetailsEach PDB model was docked using "Fit in map" in Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 4

Initial modelPDB ID:

3u5e
PDB Unreleased entry

SoftwareName: Chimera
DetailsEach PDB model was docked using "Fit in map" in Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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