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Yorodumi- EMDB-6288: Electron cryo-microscopy of fatty acid synthase (FAS) from Rhodos... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6288 | |||||||||
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Title | Electron cryo-microscopy of fatty acid synthase (FAS) from Rhodospiridium toruloides | |||||||||
Map data | Fatty acid synthase from Rhodosporidium toruloides | |||||||||
Sample |
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Keywords | Mega-enzyme / multifunctional proteins / protein assembly / acyl carrier protein / biofuel | |||||||||
Function / homology | Function and homology information : / : / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / : / holo-[acyl-carrier-protein] synthase activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity ...: / : / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / : / holo-[acyl-carrier-protein] synthase activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / hydrolase activity / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Rhodosporidium toruloides (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||
Authors | Fischer M / Rhinow D / Zhu Z / Mills DJ / Zhao ZK / Vonck J / Grininger M | |||||||||
Citation | Journal: Protein Sci / Year: 2015 Title: Cryo-EM structure of fatty acid synthase (FAS) from Rhodosporidium toruloides provides insights into the evolutionary development of fungal FAS. Authors: Manuel Fischer / Daniel Rhinow / Zhiwei Zhu / Deryck J Mills / Zongbao K Zhao / Janet Vonck / Martin Grininger / Abstract: Fungal fatty acid synthases Type I (FAS I) are up to 2.7 MDa large molecular machines composed of large multifunctional polypeptides. Half of the amino acids in fungal FAS I are involved in ...Fungal fatty acid synthases Type I (FAS I) are up to 2.7 MDa large molecular machines composed of large multifunctional polypeptides. Half of the amino acids in fungal FAS I are involved in structural elements that are responsible for scaffolding the elaborate barrel-shaped architecture and turning fungal FAS I into highly efficient de novo producers of fatty acids. Rhodosporidium toruloides is an oleaginous fungal species and renowned for its robust conversion of carbohydrates into lipids to over 70% of its dry cell weight. Here, we use cryo-EM to determine a 7.8-Å reconstruction of its FAS I that reveals unexpected features; its novel form of splitting the multifunctional polypeptide chain into the two subunits α and β, and its duplicated ACP domains. We show that the specific distribution into α and β occurs by splitting at one of many possible sites that can be accepted by fungal FAS I. While, therefore, the specific distribution in α and β chains in R. toruloides FAS I is not correlated to increased protein activities, we also show that the duplication of ACP is an evolutionary late event and argue that duplication is beneficial for the lipid overproduction phenotype. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6288.map.gz | 83.5 MB | EMDB map data format | |
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Header (meta data) | emd-6288-v30.xml emd-6288.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | 400_6288.gif 80_6288.gif | 63.9 KB 4.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6288 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6288 | HTTPS FTP |
-Validation report
Summary document | emd_6288_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_6288_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_6288_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6288 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6288 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6288.map.gz / Format: CCP4 / Size: 89 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Fatty acid synthase from Rhodosporidium toruloides | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Fatty acid synthase from Rhodospiridium toruloides
Entire | Name: Fatty acid synthase from Rhodospiridium toruloides |
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Components |
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-Supramolecule #1000: Fatty acid synthase from Rhodospiridium toruloides
Supramolecule | Name: Fatty acid synthase from Rhodospiridium toruloides / type: sample / ID: 1000 / Oligomeric state: a6b6 heterododecameric complex / Number unique components: 2 |
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Molecular weight | Experimental: 2.7 MDa / Theoretical: 2.7 MDa |
-Macromolecule #1: Fatty acid synthase subunit alpha, fungi type
Macromolecule | Name: Fatty acid synthase subunit alpha, fungi type / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Oligomeric state: a6b6 / Recombinant expression: Yes |
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Source (natural) | Organism: Rhodosporidium toruloides (fungus) |
Molecular weight | Theoretical: 318 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: 3-oxoacyl-[acyl-carrier-protein] reductase InterPro: 4'-phosphopantetheinyl transferase domain, Acyl transferase domain superfamily, Holo-[acyl carrier protein] synthase, Acyl transferase, Acyl transferase/acyl hydrolase/lysophospholipase, ...InterPro: 4'-phosphopantetheinyl transferase domain, Acyl transferase domain superfamily, Holo-[acyl carrier protein] synthase, Acyl transferase, Acyl transferase/acyl hydrolase/lysophospholipase, Fatty acid synthase, HotDog domain superfamily, Beta-ketoacyl synthase, active site, Beta-ketoacyl synthase, C-terminal, Beta-ketoacyl synthase, N-terminal, MaoC-like dehydratase domain, NAD(P)-binding domain, Phosphopantetheine-protein transferase domain, Thiolase-like, INTERPRO: IPR016038 |
-Macromolecule #2: Fatty acid synthase subunit beta, fungi type
Macromolecule | Name: Fatty acid synthase subunit beta, fungi type / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Oligomeric state: a6b6 / Recombinant expression: Yes |
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Source (natural) | Organism: Rhodosporidium toruloides (fungus) |
Molecular weight | Theoretical: 137 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Fatty acid synthase subunit beta, fungi type InterPro: Acyl transferase domain superfamily, Acyl transferase/acyl hydrolase/lysophospholipase, Aldolase-type TIM barrel, Fatty acid synthase beta subunit AflB /Fas1-like, central domain, Fatty acid synthase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.3 mg/mL |
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Buffer | pH: 7.2 / Details: 100 mM sodium phosphate, 200 mM NaCl, 1 mM EDTA |
Grid | Details: Quantifoil R2/2 holey carbon grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Details | 24-frame movies |
Date | Dec 2, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 70 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 106000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | The reconstruction was done using Relion. |
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CTF correction | Details: Each image |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 3296 |
-Atomic model buiding 1
Initial model | PDB ID: 2uvb |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: 2uva |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |