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- EMDB-2238: Cryo-EM Structure of the Mycobacterial Fatty Acid Synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-2238
TitleCryo-EM Structure of the Mycobacterial Fatty Acid Synthase
Map dataStructure of the Mycobacterial Fatty Acid Synthase
Sample
  • Sample: Mycobacterial Fatty Acid Synthase, FAS I
  • Protein or peptide: Mycobacterial Fatty Acid Synthase I
Keywordsmycobacterium / fatty acid synthase / mycolic acid biosynthesis
Function / homology
Function and homology information


fatty acid synthase complex / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid synthase activity / fatty acid biosynthetic process / hydrolase activity
Similarity search - Function
: / Fatty acid synthase central AT domain / DNA polymerase beta N-terminal domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase type I, helical / : / Fatty acid synthase type I helical domain / : / Fatty acid synthase ...: / Fatty acid synthase central AT domain / DNA polymerase beta N-terminal domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase type I, helical / : / Fatty acid synthase type I helical domain / : / Fatty acid synthase / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / HotDog domain superfamily / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesMycobacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsBoehringer D / Ban N / Leibundgut M
CitationJournal: J Mol Biol / Year: 2013
Title: 7.5-Å cryo-em structure of the mycobacterial fatty acid synthase.
Authors: Daniel Boehringer / Nenad Ban / Marc Leibundgut /
Abstract: The mycobacterial fatty acid synthase (FAS) complex is a giant 2.0-MDa α(6) homohexameric multifunctional enzyme that catalyzes synthesis of fatty acid precursors of mycolic acids, which are major ...The mycobacterial fatty acid synthase (FAS) complex is a giant 2.0-MDa α(6) homohexameric multifunctional enzyme that catalyzes synthesis of fatty acid precursors of mycolic acids, which are major components of the cell wall in Mycobacteria and play an important role in pathogenicity. Here, we present a three-dimensional reconstruction of the Mycobacterium smegmatis FAS complex at 7.5Å, highly homologous to the Mycobacterium tuberculosis multienzyme, by cryo-electron microscopy. Based on the obtained structural data, which allowed us to identify secondary-structure elements, and sequence homology with the fungal FAS, we generated an accurate architectural model of the complex. The FAS system from Mycobacteria resembles a minimized version of the fungal FAS with much larger openings in the reaction chambers. These architectural features of the mycobacterial FAS may be important for the interaction with mycolic acid processing and condensing enzymes that further modify the precursors produced by FAS and for autoactivation of the FAS complex.
History
DepositionDec 5, 2012-
Header (metadata) releaseDec 19, 2012-
Map releaseJan 16, 2013-
UpdateFeb 27, 2013-
Current statusFeb 27, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v8l
  • Surface level: 2.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2238.tif

Downloads & links

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Map

FileDownload / File: emd_2238.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the Mycobacterial Fatty Acid Synthase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.45 Å/pix.
x 160 pix.
= 392. Å		2.45 Å/pix.
x 160 pix.
= 392. Å		2.45 Å/pix.
x 160 pix.
= 392. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.7 / Movie #1: 2.7
Minimum - Maximum-7.79319286 - 14.93623257
Average (Standard dev.)-0.13342369 (±1.07625365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 392.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.452.452.45
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z392.000392.000392.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-7.79314.936-0.133

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Supplemental data

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Sample components

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Entire : Mycobacterial Fatty Acid Synthase, FAS I

EntireName: Mycobacterial Fatty Acid Synthase, FAS I
Components
  • Sample: Mycobacterial Fatty Acid Synthase, FAS I
  • Protein or peptide: Mycobacterial Fatty Acid Synthase I

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Supramolecule #1000: Mycobacterial Fatty Acid Synthase, FAS I

SupramoleculeName: Mycobacterial Fatty Acid Synthase, FAS I / type: sample / ID: 1000 / Oligomeric state: hexamer / Number unique components: 1
Molecular weightExperimental: 2 MDa / Theoretical: 2 MDa

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Macromolecule #1: Mycobacterial Fatty Acid Synthase I

MacromoleculeName: Mycobacterial Fatty Acid Synthase I / type: protein_or_peptide / ID: 1 / Name.synonym: FAS I / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: No
Source (natural)Organism: Mycobacterium smegmatis (bacteria) / Strain: mc2 155 / Location in cell: Cytosol
SequenceGO: fatty acid synthase complex / InterPro: Fatty acid synthase

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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

Concentration1.65 mg/mL
BufferpH: 7.2
Details: 100mM potassium phosphate buffer pH 7.2, 165 mM NaCl, 2mM EDTA, 2mM DTT
GridDetails: Quantifoil R2/1 200 mesh copper grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 79 K
DetailsData were collected using the automated image acquisition software FEI EPU.
DateOct 19, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Number real images: 1556 / Average electron dose: 20 e/Å2
Details: Data were collected using the automated image acquisition software FEI EPU.
Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each image
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic-5, Spider
Details: Fourier amplitudes of the reconstruction were enhanced using amplitudes from the x-ray structure of the S. cerevisiae FAS; subsequently, the map was filtered using a Butterworth low-pass filter in SPIDER
Number images used: 106884

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Atomic model buiding 1

Initial modelPDB ID:

2uv8

SoftwareName: Chimera
DetailsProtocol: Domains were separately fitted as rigid bodies and manually adjusted in O. The model was minimized with PHENIX.PDBTOOLS. Domains were separately fitted as rigid bodies and manually adjusted in O.The model was minimized with PHENIX.PDBTOOLS.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-4v8l:
Cryo-EM Structure of the Mycobacterial Fatty Acid Synthase

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