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- PDB-8psp: Asymmetric unit of the yeast fatty acid synthase in rotated state... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8psp | ||||||
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Title | Asymmetric unit of the yeast fatty acid synthase in rotated state with ACP at the acetyl transferase domain (FASx sample) | ||||||
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![]() | CYTOSOLIC PROTEIN / Fatty acid synthase / acyl carrier protein / FAS / ACP | ||||||
Function / homology | ![]() fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase activity / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / : ...fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase activity / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / : / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / holo-[acyl-carrier-protein] synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / 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 / fatty acid synthase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
![]() | Singh, K. / Bunzel, G. / Graf, B. / Yip, K.M. / Stark, H. / Chari, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Reconstruction of a fatty acid synthesis cycle from acyl carrier protein and cofactor structural snapshots. Authors: Kashish Singh / Georg Bunzel / Benjamin Graf / Ka Man Yip / Meina Neumann-Schaal / Holger Stark / Ashwin Chari / ![]() Abstract: Fatty acids (FAs) play a central metabolic role in living cells as constituents of membranes, cellular energy reserves, and second messenger precursors. A 2.6 MDa FA synthase (FAS), where the ...Fatty acids (FAs) play a central metabolic role in living cells as constituents of membranes, cellular energy reserves, and second messenger precursors. A 2.6 MDa FA synthase (FAS), where the enzymatic reactions and structures are known, is responsible for FA biosynthesis in yeast. Essential in the yeast FAS catalytic cycle is the acyl carrier protein (ACP) that actively shuttles substrates, biosynthetic intermediates, and products from one active site to another. We resolve the S. cerevisiae FAS structure at 1.9 Å, elucidating cofactors and water networks involved in their recognition. Structural snapshots of ACP domains bound to various enzymatic domains allow the reconstruction of a full yeast FA biosynthesis cycle. The structural information suggests that each FAS functional unit could accommodate exogenous proteins to incorporate various enzymatic activities, and we show proof-of-concept experiments where ectopic proteins are used to modulate FAS product profiles. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 779.1 KB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 17859MC ![]() 8prvC ![]() 8prwC ![]() 8ps1C ![]() 8ps2C ![]() 8ps8C ![]() 8ps9C ![]() 8psaC ![]() 8psfC ![]() 8psgC ![]() 8psjC ![]() 8pskC ![]() 8pslC ![]() 8psmC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 207184.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P19097, fatty-acyl-CoA synthase system, 3-oxoacyl-[acyl-carrier-protein] reductase, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Protein | | Mass: 228940.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S- ...References: UniProt: P07149, 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-PNS / | #4: Chemical | ChemComp-FMN / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Yeast fatty acid synthase / Type: COMPLEX / Entity ID: #2 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196527 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.9→183.57 Å / Cor.coef. Fo:Fc: 0.89 / SU B: 7.758 / SU ML: 0.139 / ESU R: 0.222 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.753 Å2
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Refinement step | Cycle: 1 / Total: 29695 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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