+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1623 | |||||||||
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Title | Cerulenin-inhibited type I yeast Fatty Acid Synthase | |||||||||
Map data | This is a cryo-EM map of cerulenin inhibited yeast FAS filtered to 5.9A resolution. | |||||||||
Sample |
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Keywords | fatty acid synthase / type I fungal FAS mechanism / yeast / fatty acid synthesis. | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | |||||||||
Authors | Gipson P / Mills DJ / Wouts R / Grininger M / Vonck J / Kuehlbrandt W | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2010 Title: Direct structural insight into the substrate-shuttling mechanism of yeast fatty acid synthase by electron cryomicroscopy. Authors: Preeti Gipson / Deryck J Mills / Remco Wouts / Martin Grininger / Janet Vonck / Werner Kühlbrandt / Abstract: Yeast fatty acid synthase (FAS) is a 2.6-MDa barrel-shaped multienzyme complex, which carries out cyclic synthesis of fatty acids. By electron cryomicroscopy of single particles we obtained a three- ...Yeast fatty acid synthase (FAS) is a 2.6-MDa barrel-shaped multienzyme complex, which carries out cyclic synthesis of fatty acids. By electron cryomicroscopy of single particles we obtained a three-dimensional map of yeast FAS at 5.9-A resolution. Compared to the crystal structures of fungal FAS, the EM map reveals major differences and new features that indicate a considerably different arrangement of the complex in solution compared to the crystal structures, as well as a high degree of variance inside the barrel. Distinct density regions in the reaction chambers next to each of the catalytic domains fitted the substrate-binding acyl carrier protein (ACP) domain. In each case, this resulted in the expected distance of approximately 18 A from the ACP substrate-binding site to the active site of the catalytic domains. The multiple, partially occupied positions of the ACP within the reaction chamber provide direct structural insight into the substrate-shuttling mechanism of fatty acid synthesis in this large cellular machine. | |||||||||
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_1623.map.gz | 92.7 MB | EMDB map data format | |
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Header (meta data) | emd-1623-v30.xml emd-1623.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
Images | FAS-1000dpi.tiff FAS-emdb.tif | 732.9 KB 396.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1623 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1623 | HTTPS FTP |
-Validation report
Summary document | emd_1623_validation.pdf.gz | 271.4 KB | Display | EMDB validaton report |
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Full document | emd_1623_full_validation.pdf.gz | 270.5 KB | Display | |
Data in XML | emd_1623_validation.xml.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1623 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1623 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1623.map.gz / Format: CCP4 / Size: 96.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a cryo-EM map of cerulenin inhibited yeast FAS filtered to 5.9A resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 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 : Cerulenin-inhibited Yeast FAS
Entire | Name: Cerulenin-inhibited Yeast FAS |
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Components |
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-Supramolecule #1000: Cerulenin-inhibited Yeast FAS
Supramolecule | Name: Cerulenin-inhibited Yeast FAS / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 2.6 MDa |
-Macromolecule #1: Type I yeast FAS
Macromolecule | Name: Type I yeast FAS / type: protein_or_peptide / ID: 1 / Name.synonym: yeast FAS / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Plunger |
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-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 1.19 µm / Number real images: 150 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each partilce |
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Final reconstruction | Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: OTHER / Software - Name: EMAN1 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | Automatic rigid body fits |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |