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Yorodumi- EMDB-21490: Influenza hemagglutinin trimer preprocessed with automatic workflow -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21490 | |||||||||
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Title | Influenza hemagglutinin trimer preprocessed with automatic workflow | |||||||||
Map data | Cryo-EM structure of HA trimer (EMPIAR-10175) using automatic preprocessing workflow | |||||||||
Sample |
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Biological species | unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Li Y / Cianfrocco MA | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Structure / Year: 2020 Title: High-Throughput Cryo-EM Enabled by User-Free Preprocessing Routines. Authors: Yilai Li / Jennifer N Cash / John J G Tesmer / Michael A Cianfrocco / Abstract: Single-particle cryoelectron microscopy (cryo-EM) continues to grow into a mainstream structural biology technique. Recent developments in data collection strategies alongside new sample preparation ...Single-particle cryoelectron microscopy (cryo-EM) continues to grow into a mainstream structural biology technique. Recent developments in data collection strategies alongside new sample preparation devices herald a future where users will collect multiple datasets per microscope session. To make cryo-EM data processing more automatic and user-friendly, we have developed an automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep-learning and image-analysis tools. We have verified the performance of this pipeline on a number of datasets and extended its scope to include sample screening by the user-free assessment of the qualities of a series of datasets under different conditions. We propose that our workflow provides a decision-free solution for cryo-EM, making data preprocessing more generalized and robust in the high-throughput era as well as more convenient for users from a range of backgrounds. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21490.map.gz | 27.1 MB | EMDB map data format | |
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Header (meta data) | emd-21490-v30.xml emd-21490.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
Images | emd_21490.png | 57.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21490 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21490 | HTTPS FTP |
-Validation report
Summary document | emd_21490_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_21490_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_21490_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21490 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21490 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21490.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of HA trimer (EMPIAR-10175) using automatic preprocessing workflow | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.275 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Influenza hemagglutinin trimer
Entire | Name: Influenza hemagglutinin trimer |
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Components |
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-Supramolecule #1: Influenza hemagglutinin trimer
Supramolecule | Name: Influenza hemagglutinin trimer / type: complex / ID: 1 / Parent: 0 Details: A/Hong Kong/1/1968 (H3N2), obtained commercially from MyBioSource, catalog MBS434205 |
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Source (natural) | Organism: unidentified (others) |
Recombinant expression | Organism: unidentified (others) |
Molecular weight | Theoretical: 150 KDa |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 73.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 167788 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |