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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13093 | |||||||||
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Title | Immature 60S Ribosomal Subunit from C. thermophilum | |||||||||
![]() | Immature 60S Ribosomal Subunit from C.thermophilum, Main Map | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.52 Å | |||||||||
![]() | Skalidis I / Kastritis PL | |||||||||
![]() | ![]() Title: Cryo-EM and artificial intelligence visualize endogenous protein community members. Authors: Ioannis Skalidis / Fotis L Kyrilis / Christian Tüting / Farzad Hamdi / Grzegorz Chojnowski / Panagiotis L Kastritis / ![]() Abstract: Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and ...Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and thioesters of coenzyme-A synthesis. Metabolons are highly heterogeneous due to their function, making their analysis particularly challenging. Here, we simultaneously characterize metabolon-embedded architectures of a 60S pre-ribosome, fatty acid synthase, and pyruvate/oxoglutarate dehydrogenase complex E2 cores de novo. Cryo-electron microscopy (cryo-EM) 3D reconstructions are resolved at 3.84-4.52 Å resolution by collecting <3,000 micrographs of a single cellular fraction. After combining cryo-EM with artificial intelligence-based atomic modeling and de novo sequence identification methods, at this resolution range, polypeptide hydrogen bonding patterns are discernible. Residing molecular components resemble their purified counterparts from other eukaryotes but also exhibit substantial conformational variation with potential functional implications. Our results propose an integrated tool, boosted by machine learning, that opens doors for structural systems biology spearheaded by cryo-EM characterization of native cell extracts. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.4 KB 31.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 61.1 KB | ||
Others | ![]() ![]() ![]() | 117.2 MB 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q5qC ![]() 7q5rC ![]() 7q5sC C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 1.1 TB Data #1: Unaligned fractions saved by Falcon 3 EC camera [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Immature 60S Ribosomal Subunit from C.thermophilum, Main Map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5678 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Signature 4 Map
File | emd_13093_additional_1.map | ||||||||||||
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Annotation | Signature 4 Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Immature 60S Ribosomal Subunit from C.thermophilum, Half-Map A
File | emd_13093_half_map_1.map | ||||||||||||
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Annotation | Immature 60S Ribosomal Subunit from C.thermophilum, Half-Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Immature 60S Ribosomal Subunit from C.thermophilum, Half-Map B
File | emd_13093_half_map_2.map | ||||||||||||
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Annotation | Immature 60S Ribosomal Subunit from C.thermophilum, Half-Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Native 60-mer core of Pyruvate Dehydrogenase Complex
+Supramolecule #1: Native 60-mer core of Pyruvate Dehydrogenase Complex
+Macromolecule #1: uL13
+Macromolecule #2: eL21
+Macromolecule #3: eL13
+Macromolecule #4: eL15
+Macromolecule #5: eL18
+Macromolecule #6: uL15
+Macromolecule #7: eL36
+Macromolecule #8: eL32
+Macromolecule #9: eL20
+Macromolecule #10: uL22
+Macromolecule #11: eL8
+Macromolecule #12: uL29
+Macromolecule #13: uL6
+Macromolecule #14: eL6
+Macromolecule #15: uL5
+Macromolecule #16: uL18
+Macromolecule #17: eL14
+Macromolecule #18: uL30
+Macromolecule #19: eL33
+Macromolecule #20: uL24
+Macromolecule #21: uL4
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 200.0 mM / Component - Formula: NH4CH2COOH / Component - Name: Ammonium acetate |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: For plunging, blot force 0 and blotting time of 4 sec were applied.. |
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Electron microscopy
Microscope | TFS GLACIOS |
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Temperature | Min: 77.15 K / Max: 103.15 K |
Alignment procedure | Coma free - Residual tilt: 14.7 mrad |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 2808 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 92000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |