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- EMDB-1338: Structure of fungal fatty acid synthase and implications for iter... -

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Basic information

Entry
Database: EMDB / ID: EMD-1338
TitleStructure of fungal fatty acid synthase and implications for iterative substrate shuttling.
Map datamacromolecular complex
Sample
  • Sample: fatty acid synthase from Thermomyces lanuginosus
  • Protein or peptide: fatty acid synthase
Biological speciesThermomyces lanuginosus (fungus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 15.0 Å
AuthorsBoehringer D
CitationJournal: Science / Year: 2007
Title: Structure of fungal fatty acid synthase and implications for iterative substrate shuttling.
Authors: Simon Jenni / Marc Leibundgut / Daniel Boehringer / Christian Frick / Bohdan Mikolásek / Nenad Ban /
Abstract: We report crystal structures of the 2.6-megadalton alpha6beta6 heterododecameric fatty acid synthase from Thermomyces lanuginosus at 3.1 angstrom resolution. The alpha and beta polypeptide chains ...We report crystal structures of the 2.6-megadalton alpha6beta6 heterododecameric fatty acid synthase from Thermomyces lanuginosus at 3.1 angstrom resolution. The alpha and beta polypeptide chains form the six catalytic domains required for fatty acid synthesis and numerous expansion segments responsible for extensive intersubunit connections. Detailed views of all active sites provide insights into substrate specificities and catalytic mechanisms and reveal their unique characteristics, which are due to the integration into the multienzyme. The mode of acyl carrier protein attachment in the reaction chamber, together with the spatial distribution of active sites, suggests that iterative substrate shuttling is achieved by a relatively restricted circular motion of the carrier domain in the multifunctional enzyme.
History
DepositionMar 9, 2007-
Header (metadata) releaseMar 9, 2007-
Map releaseMar 9, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.087870108
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.087870108
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v58
  • Surface level: 0.0879
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1338.gif

Downloads & links

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Map

FileDownload / File: emd_1338.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmacromolecular complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.39 Å/pix.
x 120 pix.
= 406.4 Å		3.39 Å/pix.
x 120 pix.
= 406.4 Å		3.39 Å/pix.
x 120 pix.
= 406.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.38667 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0931 / Movie #1: 0.0878701
Minimum - Maximum-0.689567 - 0.728768
Average (Standard dev.)-0.000235642 (±0.0983397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 406.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.38666666666673.38666666666673.3866666666667
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z406.400406.400406.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.6900.729-0.000

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Supplemental data

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Sample components

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Entire : fatty acid synthase from Thermomyces lanuginosus

EntireName: fatty acid synthase from Thermomyces lanuginosus
Components
  • Sample: fatty acid synthase from Thermomyces lanuginosus
  • Protein or peptide: fatty acid synthase

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Supramolecule #1000: fatty acid synthase from Thermomyces lanuginosus

SupramoleculeName: fatty acid synthase from Thermomyces lanuginosus / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: fatty acid synthase

MacromoleculeName: fatty acid synthase / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Thermomyces lanuginosus (fungus)
Molecular weightExperimental: 2.6 MDa / Theoretical: 2.6 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE / Details: native cryo
GridDetails: perforated carbon foil on 200 mesh copper grid
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJun 15, 2006
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 24 / Bits/pixel: 12
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: global
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: Imagic-5 / Number images used: 4050

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