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- EMDB-1623: Cerulenin-inhibited type I yeast Fatty Acid Synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-1623
TitleCerulenin-inhibited type I yeast Fatty Acid Synthase
Map dataThis is a cryo-EM map of cerulenin inhibited yeast FAS filtered to 5.9A resolution.
Sample
  • Sample: Cerulenin-inhibited Yeast FAS
  • Protein or peptide: Type I yeast FAS
Keywordsfatty acid synthase / type I fungal FAS mechanism / yeast / fatty acid synthesis.
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsGipson P / Mills DJ / Wouts R / Grininger M / Vonck J / Kuehlbrandt W
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Direct structural insight into the substrate-shuttling mechanism of yeast fatty acid synthase by electron cryomicroscopy.
Authors: Preeti Gipson / Deryck J Mills / Remco Wouts / Martin Grininger / Janet Vonck / Werner Kühlbrandt /
Abstract: Yeast fatty acid synthase (FAS) is a 2.6-MDa barrel-shaped multienzyme complex, which carries out cyclic synthesis of fatty acids. By electron cryomicroscopy of single particles we obtained a three- ...Yeast fatty acid synthase (FAS) is a 2.6-MDa barrel-shaped multienzyme complex, which carries out cyclic synthesis of fatty acids. By electron cryomicroscopy of single particles we obtained a three-dimensional map of yeast FAS at 5.9-A resolution. Compared to the crystal structures of fungal FAS, the EM map reveals major differences and new features that indicate a considerably different arrangement of the complex in solution compared to the crystal structures, as well as a high degree of variance inside the barrel. Distinct density regions in the reaction chambers next to each of the catalytic domains fitted the substrate-binding acyl carrier protein (ACP) domain. In each case, this resulted in the expected distance of approximately 18 A from the ACP substrate-binding site to the active site of the catalytic domains. The multiple, partially occupied positions of the ACP within the reaction chamber provide direct structural insight into the substrate-shuttling mechanism of fatty acid synthesis in this large cellular machine.
History
DepositionJun 15, 2009-
Header (metadata) releaseJun 22, 2009-
Map releaseJun 11, 2010-
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: 2.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

FAS-1000dpi....

FAS-emdb.tif

Downloads & links

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Map

FileDownload / File: emd_1623.map.gz / Format: CCP4 / Size: 96.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cryo-EM map of cerulenin inhibited yeast FAS filtered to 5.9A resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 296 pix.
= 337.44 Å		1.14 Å/pix.
x 296 pix.
= 337.44 Å		1.14 Å/pix.
x 296 pix.
= 337.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.3 / Movie #1: 2.3
Minimum - Maximum-11.6372 - 13.516999999999999
Average (Standard dev.)0.0508731 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-148-148-148
Dimensions296296296
Spacing296296296
CellA=B=C: 337.44 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z296296296
origin x/y/z0.0000.0000.000
length x/y/z337.440337.440337.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS-148-148-148
NC/NR/NS296296296
D min/max/mean-11.63713.5170.051

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Supplemental data

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Sample components

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Entire : Cerulenin-inhibited Yeast FAS

EntireName: Cerulenin-inhibited Yeast FAS
Components
  • Sample: Cerulenin-inhibited Yeast FAS
  • Protein or peptide: Type I yeast FAS

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Supramolecule #1000: Cerulenin-inhibited Yeast FAS

SupramoleculeName: Cerulenin-inhibited Yeast FAS / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 2.6 MDa

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Macromolecule #1: Type I yeast FAS

MacromoleculeName: Type I yeast FAS / type: protein_or_peptide / ID: 1 / Name.synonym: yeast FAS / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker'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

VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Plunger

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 1.19 µm / Number real images: 150 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each partilce
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: OTHER / Software - Name: EMAN1

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Atomic model buiding 1

Initial modelPDB ID:

2vkz

SoftwareName: Chimera
DetailsAutomatic rigid body fits
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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