+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7624 | |||||||||
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Title | Hemagglutinin with spot-to-plunge time of 800ms | |||||||||
Map data | Hemagglutinin with spot-to-plunge time of 800ms | |||||||||
Sample |
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Biological species | unidentified (others) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Noble AJ / Wei H / Dandey VP / Zhang Z / Potter CS / Carragher B | |||||||||
Citation | Journal: Nat Methods / Year: 2018 Title: Reducing effects of particle adsorption to the air-water interface in cryo-EM. Authors: Alex J Noble / Hui Wei / Venkata P Dandey / Zhening Zhang / Yong Zi Tan / Clinton S Potter / Bridget Carragher / Abstract: Most protein particles prepared in vitreous ice for single-particle cryo-electron microscopy (cryo-EM) are adsorbed to air-water or substrate-water interfaces, which can cause the particles to adopt ...Most protein particles prepared in vitreous ice for single-particle cryo-electron microscopy (cryo-EM) are adsorbed to air-water or substrate-water interfaces, which can cause the particles to adopt preferred orientations. By using a rapid plunge-freezing robot and nanowire grids, we were able to reduce some of the deleterious effects of the air-water interface by decreasing the dwell time of particles in thin liquid films. We demonstrated this by using single-particle cryo-EM and cryo-electron tomography (cryo-ET) to examine hemagglutinin, insulin receptor complex, and apoferritin. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7624.map.gz | 3.2 GB | EMDB map data format | |
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Header (meta data) | emd-7624-v30.xml emd-7624.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | emd_7624.png | 409.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7624 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7624 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7624.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Hemagglutinin with spot-to-plunge time of 800ms | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.34 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 : Hemagglutinin
Entire | Name: Hemagglutinin |
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Components |
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-Supramolecule #1: Hemagglutinin
Supramolecule | Name: Hemagglutinin / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: unidentified (others) |
Recombinant expression | Organism: unidentified (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 0.0001 |
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Grid | Model: Homemade |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER Details: The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', ...Details: The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', 'HOMEMADE PLUNGER', 'REICHERT-JUNG PLUNGER', 'FEI VITROBOT MARK I', 'LEICA KF80', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'OTHER', 'FEI VITROBOT MARK IV']) so OTHER is written into the XML file. |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm |
Specialist optics | Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Average electron dose: 3.0 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: TOMO3D / Software - details: SIRT, 30 iterations / Number images used: 30 |
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