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- PDB-6u5w: Electron cryomicroscopy structure of C. albicans FAS in the KS-st... -

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Basic information

Entry
Database: PDB / ID: 6u5w
TitleElectron cryomicroscopy structure of C. albicans FAS in the KS-stalled state
Components
  • Fatty acid synthase subunit alpha
  • Fatty acid synthase subunit beta
KeywordsTRANSFERASE / Fungal Fatty acid synthase
Function / homology
Function and homology information


mitotic nuclear membrane biogenesis / palmitic acid biosynthetic process / : / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity ...mitotic nuclear membrane biogenesis / palmitic acid biosynthetic process / : / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / holo-[acyl-carrier-protein] synthase activity / fatty acid synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / long-chain fatty acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / cytosol
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #120 / Transcription Elongation Factor S-II; Chain A - #70 / Lipocalin - #700 / Arylsulfatase, C-terminal domain - #100 / Alpha-Beta Plaits - #3320 / Alpha-Beta Plaits - #3330 / Helix Hairpins - #1400 / Hydrophobic Seed Protein / Hydrophobic Seed Protein - #10 / : ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #120 / Transcription Elongation Factor S-II; Chain A - #70 / Lipocalin - #700 / Arylsulfatase, C-terminal domain - #100 / Alpha-Beta Plaits - #3320 / Alpha-Beta Plaits - #3330 / Helix Hairpins - #1400 / Hydrophobic Seed Protein / Hydrophobic Seed Protein - #10 / : / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Fatty acid synthase / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / MaoC-like dehydratase domain / MaoC like domain / Arylsulfatase, C-terminal domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Transcription Elongation Factor S-II; Chain A / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / 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 / Ketosynthase family 3 (KS3) domain profile. / Helix Hairpins / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Phosphopantetheine attachment site. / Thiolase-like / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Lipocalin / Helix non-globular / Special / Aldolase class I / Aldolase-type TIM barrel / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Fatty acid synthase subunit beta / Fatty acid synthase subunit alpha
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLou, J.W. / Mazhab-Jafari, M.T.
CitationJournal: Sci Rep / Year: 2019
Title: Electron cryomicroscopy observation of acyl carrier protein translocation in type I fungal fatty acid synthase.
Authors: Jennifer W Lou / Kali R Iyer / S M Naimul Hasan / Leah E Cowen / Mohammad T Mazhab-Jafari /
Abstract: During fatty acid biosynthesis, acyl carrier proteins (ACPs) from type I fungal fatty acid synthase (FAS) shuttle substrates and intermediates within a reaction chamber that hosts multiple spatially- ...During fatty acid biosynthesis, acyl carrier proteins (ACPs) from type I fungal fatty acid synthase (FAS) shuttle substrates and intermediates within a reaction chamber that hosts multiple spatially-fixed catalytic centers. A major challenge in understanding the mechanism of ACP-mediated substrate shuttling is experimental observation of its transient interaction landscape within the reaction chamber. Here, we have shown that ACP spatial distribution is sensitive to the presence of substrates in a catalytically inhibited state, which enables high-resolution investigation of the ACP-dependent conformational transitions within the enoyl reductase (ER) reaction site. In two fungal FASs with distinct ACP localization, the shuttling domain is targeted to the ketoacyl-synthase (KS) domain and away from other catalytic centers, such as acetyl-transferase (AT) and ER domains by steric blockage of the KS active site followed by addition of substrates. These studies strongly suggest that acylation of phosphopantetheine arm of ACP may be an integral part of the substrate shuttling mechanism in type I fungal FAS.
History
DepositionAug 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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Assembly

Deposited unit
A: Fatty acid synthase subunit alpha
B: Fatty acid synthase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)420,3835
Polymers418,4402
Non-polymers1,9433
Water0
1
A: Fatty acid synthase subunit alpha
B: Fatty acid synthase subunit beta
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)2,522,29630
Polymers2,510,63812
Non-polymers11,65918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D3 (2x3 fold dihedral))

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Components

#1: Protein Fatty acid synthase subunit alpha /


Mass: 190261.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)
References: UniProt: P43098, fatty-acyl-CoA synthase system, 3-oxoacyl-[acyl-carrier-protein] reductase, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein Fatty acid synthase subunit beta /


Mass: 228177.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)
References: UniProt: P34731, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S- ...References: UniProt: P34731, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, oleoyl-[acyl-carrier-protein] hydrolase
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Fatty acid synthase / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 2.6 MDa / Experimental value: NO
Source (natural)Organism: Candida albicans (yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 43 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC2particle selection
2EPU1.11.0image acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10cryoSPARC2initial Euler assignment
11cryoSPARC2final Euler assignment
13cryoSPARC23D reconstruction
CTF correctionDetails: CTFFIND4 within cryoSPARC2 / Type: NONE
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24417 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 2UV8

2uv8


Accession code: 2UV8 / Source name: PDB / Type: experimental model

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