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

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Basic information

Entry
Database: PDB / ID: 4v8l
TitleCryo-EM Structure of the Mycobacterial Fatty Acid Synthase
ComponentsFATTY ACID SYNTHASE
KeywordsTRANSFERASE / MYCOLIC ACID BIOSYNTHESIS / MULTIFUNCTIONAL ENZYME / SUBSTRATE CHANNELING
Function / homology
Function and homology information


fatty acid synthase complex / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / hydrolase activity
Similarity search - Function
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 / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / MaoC-like dehydratase 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 / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Beta-ketoacyl synthase / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / 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
FLAVIN MONONUCLEOTIDE / Fatty acid synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodELECTRON MICROSCOPY / single 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 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4B3Y, 3ZEN
Revision 1.1Dec 10, 2014Group: Other
Revision 2.0Aug 2, 2017Group: Atomic model / Data collection / Refinement description
Category: atom_site / em_3d_fitting / em_software
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id
Revision 2.1Aug 21, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 2.2Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "ED" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2238
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,957,28812
Polymers1,954,5506
Non-polymers2,7386
Water0
1


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

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Components

#1: Protein
FATTY ACID SYNTHASE / / TYPE I FATTY ACID SYNTHASE / MYCOBACTERIAL FATTY ACID SYNTHASE I


Mass: 325758.250 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / References: UniProt: A0R1H7
#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: MYCOBACTERIAL FATTY ACID SYNTHASE, FAS I / Type: COMPLEX
Buffer solutionName: 100MM POTASSIUM PHOSPHATE BUFFER PH 7.2, 165 MM NACL, 2MM EDTA, 2MM DTT
pH: 7.2
Details: 100MM POTASSIUM PHOSPHATE BUFFER PH 7.2, 165 MM NACL, 2MM EDTA, 2MM DTT
SpecimenConc.: 1.65 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: VITRIFIED WITH HOMEMADE PLUNGER IN LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Oct 19, 2012
Details: DATA WERE COLLECTED USING THE AUTOMATED IMAGE ACQUISITION SOFTWARE FEI EPU.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 100000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderTemperature: 79 K / Tilt angle max: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)
Image scansNum. digital images: 1556
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2IMAGIC53D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: EACH IMAGE
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionMethod: COMMON LINES, PROJECTION MATCHING / Resolution: 7.5 Å / Num. of particles: 106884 / Nominal pixel size: 2.37 Å / Actual pixel size: 1.4 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2238 (DEPOSITION ID: 11255).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--DOMAINS WERE SEPARATELY FITTED AS RIGID BODIES AND MANUALLY ADJUSTED IN O. THE MODEL WAS MINIMIZED WITH PHENIX.PDBTOOLS. REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2UV8

2uv8

RefinementHighest resolution: 7.5 Å
Refinement stepCycle: LAST / Highest resolution: 7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63060 0 93 0 63153

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