+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36313 | |||||||||
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Title | Cryo-EM structure of apoferritin with MSBP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Iron storage / Complex / METAL BINDING PROTEIN | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.16 Å | |||||||||
Authors | Xu Y / Qin Y / Wang L / Zhang Y / Wang Y / Dang S | |||||||||
Funding support | Hong Kong, 1 items
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Citation | Journal: Commun Biol / Year: 2024 Title: Metallo-supramolecular branched polymer protects particles from air-water interface in single-particle cryo-electron microscopy. Authors: Yixin Xu / Yuqi Qin / Lang Wang / Yingyi Zhang / Yufeng Wang / Shangyu Dang / Abstract: Recent technological breakthroughs in single-particle cryo-electron microscopy (cryo-EM) enable rapid atomic structure determination of biological macromolecules. A major bottleneck in the current ...Recent technological breakthroughs in single-particle cryo-electron microscopy (cryo-EM) enable rapid atomic structure determination of biological macromolecules. A major bottleneck in the current single particle cryo-EM pipeline is the preparation of good quality frozen cryo-EM grids, which is mostly a trial-and-error process. Among many issues, preferred particle orientation and sample damage by air-water interface (AWI) are common practical problems. Here we report a method of applying metallo-supramolecular branched polymer (MSBP) in the cryo-sample preparation for high-resolution single-particle cryo-EM. Our data shows that MSBP keeps a majority of particles away from air-water interface and mitigates preferred orientation as verified by the analyses of apoferritin, hemagglutinin) trimer and various sample proteins. The use of MSBP is a simple method to improve particle distribution for high-resolution structure determination in single-particle cryo-EM. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36313.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-36313-v30.xml emd-36313.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_36313.png | 192.7 KB | ||
Masks | emd_36313_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-36313.cif.gz | 4 KB | ||
Others | emd_36313_half_map_1.map.gz emd_36313_half_map_2.map.gz | 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36313 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36313 | HTTPS FTP |
-Validation report
Summary document | emd_36313_validation.pdf.gz | 934.6 KB | Display | EMDB validaton report |
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Full document | emd_36313_full_validation.pdf.gz | 934.1 KB | Display | |
Data in XML | emd_36313_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_36313_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36313 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36313 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36313.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_36313_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36313_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36313_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Apoferritin with MSBP
Entire | Name: Apoferritin with MSBP |
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Components |
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-Supramolecule #1: Apoferritin with MSBP
Supramolecule | Name: Apoferritin with MSBP / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 255785 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |