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Yorodumi- EMDB-50580: SOLIST cryo-tomogram of native left ventricle mouse heart muscle #1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50580 | |||||||||
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Title | SOLIST cryo-tomogram of native left ventricle mouse heart muscle #1 | |||||||||
Map data | M. musculus heart muscle tomogram 1 (cross-section) | |||||||||
Sample |
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Keywords | muscle / motor protein / thick filament / thin filament | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography | |||||||||
Authors | Erdmann PS / Nguyen HTD / Perone G / Klena N / Vazzana R / Kaluthantrige Don F / Silva M / Sorrentino S / Swuec P / Leroux F ...Erdmann PS / Nguyen HTD / Perone G / Klena N / Vazzana R / Kaluthantrige Don F / Silva M / Sorrentino S / Swuec P / Leroux F / Kalebic N / Coscia F | |||||||||
Funding support | 1 items
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Citation | Journal: Structure / Year: 2023 Title: Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome. Authors: Sasha L Evans / Monsour M J Al-Hazeem / Daniel Mann / Nicolas Smetacek / Andrew J Beavil / Yaqi Sun / Taiyu Chen / Gregory F Dykes / Lu-Ning Liu / Julien R C Bergeron / Abstract: Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, ...Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating several enzymes, including ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for the first step of the Calvin-Benson-Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural understanding of native carboxysomes is currently limited to low-resolution studies. Here, we report the characterization of a native α-carboxysome from a marine cyanobacterium by single-particle cryoelectron microscopy (cryo-EM). We have determined the structure of its RuBisCO enzyme, and obtained low-resolution maps of its icosahedral shell, and of its concentric interior organization. Using integrative modeling approaches, we have proposed a complete atomic model of an intact carboxysome, providing insight into its organization and assembly. This is critical for a better understanding of the carbon fixation mechanism and toward repurposing carboxysomes in synthetic biology for biotechnological applications. #1: Journal: Nature Structural Biology / Year: 2024 Title: SOLIST cryo-tomogram of native left ventricle mouse heart muscle #1 Authors: Nguyen HTD / Perone G / Klena N / Vazzana R / Kaluthantrige Don F / Silva M / Sorrentino S / Swuec P / Leroux F / Kalebic N / Coscia F / Erdmann PS | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50580.map.gz | 235.9 MB | EMDB map data format | |
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Header (meta data) | emd-50580-v30.xml emd-50580.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_50580.png | 283.4 KB | ||
Filedesc metadata | emd-50580.cif.gz | 4.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50580 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50580 | HTTPS FTP |
-Validation report
Summary document | emd_50580_validation.pdf.gz | 532.9 KB | Display | EMDB validaton report |
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Full document | emd_50580_full_validation.pdf.gz | 532.4 KB | Display | |
Data in XML | emd_50580_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | emd_50580_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50580 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50580 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_50580.map.gz / Format: CCP4 / Size: 256 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Annotation | M. musculus heart muscle tomogram 1 (cross-section) | ||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 15.624 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : In situ cryo-electron tomogram of native mouse heart muscle #1
Entire | Name: In situ cryo-electron tomogram of native mouse heart muscle #1 |
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Components |
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-Supramolecule #1: In situ cryo-electron tomogram of native mouse heart muscle #1
Supramolecule | Name: In situ cryo-electron tomogram of native mouse heart muscle #1 type: cell / ID: 1 / Parent: 0 / Details: cross-section of thick and thin filaments |
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Source (natural) | Organism: Mus musculus (house mouse) / Strain: C57BL/6 N / Organ: heart / Tissue: muscle |
-Experimental details
-Structure determination
Processing | electron tomography |
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Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. Details: glow-discharged at 30 mA for 30 s (GloQube Plus Glow discharge system, Quorum Technologies) |
Details | SOLIST lamella preparation of native mouse heart muscle |
High pressure freezing | Instrument: OTHER Details: Before use, 3 mm type A (100 micrometer well) and type B planchettes were cleaned by sonication for 5 min, 30 s on, 30 s off, 40% Amplitude on a Branson SFX 550. Type B lids were polished ...Details: Before use, 3 mm type A (100 micrometer well) and type B planchettes were cleaned by sonication for 5 min, 30 s on, 30 s off, 40% Amplitude on a Branson SFX 550. Type B lids were polished with 1 micrometer lapping paper and coated with 0.1% soy lecithin dissolved in chloroform.. The value given for _em_high_pressure_freezing.instrument is Leica EM ICE. This is not in a list of allowed values {'OTHER', 'BAL-TEC HPM 010', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT2', 'LEICA EM HPM100', 'LEICA EM PACT'} so OTHER is written into the XML file. |
Cryo protectant | 20% dextran, 5% sucrose |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 60 / Focused ion beam - Temperature: 80 K / Focused ion beam - Initial thickness: 4000 / Focused ion beam - Final thickness: 200 Focused ion beam - Details: SOLIST procedure. The value given for _em_focused_ion_beam.instrument is Aquilos 2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 41 / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 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: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: eTomo (ver. 4.11.7) / Details: final tomogram denoised with CryoCare 2.1 / Number images used: 41 |
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