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- PDB-4v8v: Structure and conformational variability of the Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 4v8v
TitleStructure and conformational variability of the Mycobacterium tuberculosis fatty acid synthase multienzyme complex
ComponentsTYPE-I FATTY ACID SYNTHASE
KeywordsHYDROLASE / CODIMENSIONAL PRINCIPAL COMPONENT ANALYSIS
Function / homologyFLAVIN MONONUCLEOTIDE
Function and homology information
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 20 Å
AuthorsCiccarelli, L. / Connell, S.R. / Enderle, M. / Mills, D.J. / 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 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4BJD, 4BJE
Revision 1.1Dec 10, 2014Group: Other
Revision 2.0Aug 2, 2017Group: Advisory / Atomic model / Data collection
Category: atom_site / em_image_scans ...atom_site / em_image_scans / em_software / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _em_software.image_processing_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Revision 2.1Dec 11, 2019Group: Other / Category: atom_sites / pdbx_database_status
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_database_status.process_site
Revision 2.2Jul 29, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: TYPE-I FATTY ACID SYNTHASE
B: TYPE-I FATTY ACID SYNTHASE
C: TYPE-I FATTY ACID SYNTHASE
D: TYPE-I FATTY ACID SYNTHASE
E: TYPE-I FATTY ACID SYNTHASE
F: TYPE-I FATTY ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,982,06612
Polymers1,979,3286
Non-polymers2,7386
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
TYPE-I FATTY ACID SYNTHASE


Mass: 329887.969 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TYPE-I FATTY ACID SYNTHASE / Type: COMPLEX
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Dec 16, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1800 nm
Image recordingFilm or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1EMAN23D reconstruction
2SPARX3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 20 Å / Num. of particles: 4337
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2358. (DEPOSITION ID: 11626).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY
Atomic model buildingPDB-ID: 4B3Y

4b3y
PDB Unreleased entry

RefinementHighest resolution: 20 Å
Refinement stepCycle: LAST / Highest resolution: 20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62835 0 93 0 62928

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