+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37156 | |||||||||
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Title | Graphene sandwiched equine spleen apoferritin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | equine spleen / storing iron / iron homeostasis / O symmetry / METAL BINDING PROTEIN | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 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_37156.map.gz | 6.6 MB | EMDB map data format | |
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Header (meta data) | emd-37156-v30.xml emd-37156.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_37156.png | 155.2 KB | ||
Masks | emd_37156_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-37156.cif.gz | 3.8 KB | ||
Others | emd_37156_half_map_1.map.gz emd_37156_half_map_2.map.gz | 20.6 MB 20.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37156 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37156 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_37156.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.856 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_37156_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37156_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37156_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : equine spleen apoferritin
Entire | Name: equine spleen apoferritin |
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Components |
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-Supramolecule #1: equine spleen apoferritin
Supramolecule | Name: equine spleen apoferritin / type: complex / ID: 1 / Parent: 0 / Details: graphene sandwiched |
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Source (natural) | Organism: Equus caballus (horse) |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9596 |