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- EMDB-0179: Cryo-EM map of the Fatty Acid Synthase from S. cerevisiae -

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Basic information

Entry
Database: EMDB / ID: EMD-0179
TitleCryo-EM map of the Fatty Acid Synthase from S. cerevisiae
Map data
Sample
  • Complex: Cryo-EM map of the Fatty Acid Synthase from S. cerevisiae
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 24.6 Å
AuthorsD'Imprima E / Floris D / Sanchez R / Joppe M / Grininger M / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Volkswagen Foundation85701 Germany
CitationJournal: Elife / Year: 2019
Title: Protein denaturation at the air-water interface and how to prevent it.
Authors: Edoardo D'Imprima / Davide Floris / Mirko Joppe / Ricardo Sánchez / Martin Grininger / Werner Kühlbrandt /
Abstract: Electron cryo-microscopy analyzes the structure of proteins and protein complexes in vitrified solution. Proteins tend to adsorb to the air-water interface in unsupported films of aqueous solution, ...Electron cryo-microscopy analyzes the structure of proteins and protein complexes in vitrified solution. Proteins tend to adsorb to the air-water interface in unsupported films of aqueous solution, which can result in partial or complete denaturation. We investigated the structure of yeast fatty acid synthase at the air-water interface by electron cryo-tomography and single-particle image processing. Around 90% of complexes adsorbed to the air-water interface are partly denatured. We show that the unfolded regions face the air-water interface. Denaturation by contact with air may happen at any stage of specimen preparation. Denaturation at the air-water interface is completely avoided when the complex is plunge-frozen on a substrate of hydrophilized graphene.
History
DepositionAug 8, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseAug 21, 2019-
UpdateAug 21, 2019-
Current statusAug 21, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.38
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.38
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0179.png

Downloads & links

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Map

FileDownload / File: emd_0179.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 140 pix.
= 308. Å		2.2 Å/pix.
x 140 pix.
= 308. Å		2.2 Å/pix.
x 140 pix.
= 308. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.38 / Movie #1: 1.38
Minimum - Maximum-0.7323146 - 2.6531134
Average (Standard dev.)0.7689236 (±0.3737751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z308.000308.000308.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.7322.6530.769

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Supplemental data

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Sample components

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Entire : Cryo-EM map of the Fatty Acid Synthase from S. cerevisiae

EntireName: Cryo-EM map of the Fatty Acid Synthase from S. cerevisiae
Components
  • Complex: Cryo-EM map of the Fatty Acid Synthase from S. cerevisiae

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Supramolecule #1: Cryo-EM map of the Fatty Acid Synthase from S. cerevisiae

SupramoleculeName: Cryo-EM map of the Fatty Acid Synthase from S. cerevisiae
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: BY.PK1238_KO
Molecular weightTheoretical: 2.6 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 24.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 836
ExtractionNumber tomograms: 11 / Number images used: 2090
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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