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- EMDB-2357: Structure and conformational variability of the Mycobacterium tub... -

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Basic information

Entry
Database: EMDB / ID: EMD-2357
TitleStructure and conformational variability of the Mycobacterium tuberculosis fatty acid synthase multienzyme complex
Map dataM. tuberculosis type-I fatty acid synthase - map 1
Sample
  • Sample: M. tuberculosis type-I fatty acid synthase
  • Protein or peptide: Type-I fatty acid synthase
KeywordsM. tuberculosis / fatty acid synthesis / sample heterogeneity / protein flexibility / codimensional principal component analysis
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.5 Å
AuthorsCiccarelli L / Connell SR / Enderle M / Mills DJ / Vonck J / Grininger M
CitationJournal: Structure / Year: 2013
Title: Structure and conformational variability of the mycobacterium tuberculosis fatty acid synthase multienzyme complex.
Authors: Luciano Ciccarelli / Sean R Connell / Mathias Enderle / Deryck J Mills / Janet Vonck / Martin Grininger /
Abstract: Antibiotic therapy in response to Mycobacterium tuberculosis infections targets de novo fatty acid biosynthesis, which is orchestrated by a 1.9 MDa type I fatty acid synthase (FAS). Here, we ...Antibiotic therapy in response to Mycobacterium tuberculosis infections targets de novo fatty acid biosynthesis, which is orchestrated by a 1.9 MDa type I fatty acid synthase (FAS). Here, we characterize M. tuberculosis FAS by single-particle cryo-electron microscopy and interpret the data by docking the molecular models of yeast and Mycobacterium smegmatis FAS. Our analysis reveals a porous barrel-like structure of considerable conformational variability that is illustrated by the identification of several conformational states with altered topology in the multienzymatic assembly. This demonstrates that the barrel-like structure of M. tuberculosis FAS is not just a static scaffold for the catalytic domains, but may play an active role in coordinating fatty acid synthesis. The conception of M. tuberculosis FAS as a highly dynamic assembly of domains revises the view on bacterial type I fatty acid synthesis and might inspire new strategies for inhibition of de novo fatty acid synthesis in M. tuberculosis.
History
DepositionApr 12, 2013-
Header (metadata) releaseApr 17, 2013-
Map releaseJun 19, 2013-
UpdateOct 12, 2016-
Current statusOct 12, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v8w
  • Surface level: 2.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2357.png

Downloads & links

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Map

FileDownload / File: emd_2357.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationM. tuberculosis type-I fatty acid synthase - map 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.28 Å/pix.
x 200 pix.
= 456. Å		2.28 Å/pix.
x 200 pix.
= 456. Å		2.28 Å/pix.
x 200 pix.
= 456. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 2.0 / Movie #1: 2.2
Minimum - Maximum-2.14870143 - 9.063332559999999
Average (Standard dev.)-0.00000001 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 456.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.282.282.28
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z456.000456.000456.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-2.1499.063-0.000

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Supplemental data

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Sample components

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Entire : M. tuberculosis type-I fatty acid synthase

EntireName: M. tuberculosis type-I fatty acid synthase
Components
  • Sample: M. tuberculosis type-I fatty acid synthase
  • Protein or peptide: Type-I fatty acid synthase

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Supramolecule #1000: M. tuberculosis type-I fatty acid synthase

SupramoleculeName: M. tuberculosis type-I fatty acid synthase / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 2.0 MDa

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Macromolecule #1: Type-I fatty acid synthase

MacromoleculeName: Type-I fatty acid synthase / type: protein_or_peptide / ID: 1 / Name.synonym: FAS / Oligomeric state: Homohexamer / Recombinant expression: Yes
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightExperimental: 2.0 MDa / Theoretical: 2.0 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

GridDetails: Quantifoils copper grid
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
DateDec 16, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 17.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2, SPARX / Number images used: 9136

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Atomic model buiding 1

Initial modelPDB ID:

3zen
PDB Unreleased entry

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v8w:
Structure and conformational variability of the Mycobacterium tuberculosis fatty acid synthase multienzyme complex

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