+Open data
-Basic information
Entry | Database: PDB / ID: 6ta1 | ||||||
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Title | Fatty acid synthase of S. cerevisiae | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / megasynthase / complex | ||||||
Function / homology | Function and homology information : / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase ...: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [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 / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / fatty acid synthase activity / (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 / mitochondrion / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Vonck, J. / D'Imprima, E. / Joppe, M. / Grininger, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: IUCrJ / Year: 2020 Title: The resolution revolution in cryoEM requires high-quality sample preparation: a rapid pipeline to a high-resolution map of yeast fatty acid synthase. Authors: Mirko Joppe / Edoardo D'Imprima / Nina Salustros / Karthik S Paithankar / Janet Vonck / Martin Grininger / Werner Kühlbrandt / Abstract: Single-particle electron cryo-microscopy (cryoEM) has undergone a 'resolution revolution' that makes it possible to characterize megadalton (MDa) complexes at atomic resolution without crystals. To ...Single-particle electron cryo-microscopy (cryoEM) has undergone a 'resolution revolution' that makes it possible to characterize megadalton (MDa) complexes at atomic resolution without crystals. To fully exploit the new opportunities in molecular microscopy, new procedures for the cloning, expression and purification of macromolecular complexes need to be explored. Macromolecular assemblies are often unstable, and invasive construct design or inadequate purification conditions and sample-preparation methods can result in disassembly or denaturation. The structure of the 2.6 MDa yeast fatty acid synthase (FAS) has been studied by electron microscopy since the 1960s. Here, a new, streamlined protocol for the rapid production of purified yeast FAS for structure determination by high-resolution cryoEM is reported. Together with a companion protocol for preparing cryoEM specimens on a hydrophilized graphene layer, the new protocol yielded a 3.1 Å resolution map of yeast FAS from 15 000 automatically picked particles within a day. The high map quality enabled a complete atomic model of an intact fungal FAS to be built. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ta1.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ta1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ta1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/6ta1 ftp://data.pdbj.org/pub/pdb/validation_reports/ta/6ta1 | HTTPS FTP |
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-Related structure data
Related structure data | 10420MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 207264.406 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: FAS2, YPL231W, P1409 / Production host: Saccharomyces cerevisiae (brewer's yeast) 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.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: FAS1, YKL182W / Production host: Saccharomyces cerevisiae (brewer's yeast) 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-NDP / #4: Chemical | ChemComp-FMN / Has ligand of interest | N | |
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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 |
-Sample preparation
Component | Name: fatty acid synthase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 2.6 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 6.5 |
Buffer component | Conc.: 100 mM / Name: sodium phosphate |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 792 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 19981 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15320 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3HMJ |