+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37158 | |||||||||
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Title | Graphene sandwiched 20S proteasome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | D7 symmetry / protein degradation / HYDROLASE | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Liu N / Xu J / Wang HW | |||||||||
Funding support | China, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Graphene sandwich-based biological specimen preparation for cryo-EM analysis. Authors: Jie Xu / Xiaoyin Gao / Liming Zheng / Xia Jia / Kui Xu / Yuwei Ma / Xiaoding Wei / Nan Liu / Hailin Peng / Hong-Wei Wang / Abstract: High-quality specimen preparation plays a crucial role in cryo-electron microscopy (cryo-EM) structural analysis. In this study, we have developed a reliable and convenient technique called the ...High-quality specimen preparation plays a crucial role in cryo-electron microscopy (cryo-EM) structural analysis. In this study, we have developed a reliable and convenient technique called the graphene sandwich method for preparing cryo-EM specimens. This method involves using two layers of graphene films that enclose macromolecules on both sides, allowing for an appropriate ice thickness for cryo-EM analysis. The graphene sandwich helps to mitigate beam-induced charging effect and reduce particle motion compared to specimens prepared using the traditional method with graphene support on only one side, therefore improving the cryo-EM data quality. These advancements may open new opportunities to expand the use of graphene in the field of biological electron microscopy. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37158.map.gz | 13.6 MB | EMDB map data format | |
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Header (meta data) | emd-37158-v30.xml emd-37158.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_37158.png | 134.9 KB | ||
Masks | emd_37158_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-37158.cif.gz | 3.8 KB | ||
Others | emd_37158_half_map_1.map.gz emd_37158_half_map_2.map.gz | 80.9 MB 81.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37158 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37158 | HTTPS FTP |
-Validation report
Summary document | emd_37158_validation.pdf.gz | 979.1 KB | Display | EMDB validaton report |
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Full document | emd_37158_full_validation.pdf.gz | 978.7 KB | Display | |
Data in XML | emd_37158_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_37158_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37158 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37158 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_37158.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8374 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_37158_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37158_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37158_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 20S proteasome
Entire | Name: 20S proteasome |
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Components |
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-Supramolecule #1: 20S proteasome
Supramolecule | Name: 20S proteasome / type: complex / ID: 1 / Parent: 0 / Details: graphene sandwiched |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 2.4 µm / Nominal defocus min: 1.3 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14392 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |