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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7628 | |||||||||
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Title | Hemagglutinin with spot-to-plunge time of 100ms | |||||||||
![]() | Hemagglutinin with spot-to-plunge time of 100ms | |||||||||
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Biological species | unidentified (others) | |||||||||
Method | electron tomography / cryo EM | |||||||||
![]() | Noble AJ / Wei H / Dandey VP / Zhang Z / Potter CS / Carragher B | |||||||||
![]() | ![]() 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 |
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Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.6 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 8 KB 8 KB | Display Display | ![]() |
Images | ![]() | 428.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 77.1 KB | Display | ![]() |
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Full document | ![]() | 76.2 KB | Display | |
Data in XML | ![]() | 500 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7623C ![]() 7624C ![]() 7625C ![]() 7627C ![]() 7629C ![]() 7630C ![]() 7788C ![]() 7791C ![]() 7792C C: citing same article ( |
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EM raw data | ![]() Data size: 21.9 / Data #1: Tilt-series image stacks [tilt series] Data #2: Appion-Protomo tilt-series alignments [tilt series]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Hemagglutinin with spot-to-plunge time of 100ms | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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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![]() | electron tomography |
Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: TOMO3D / Software - details: SIRT, 30 iterations / Number images used: 30 |
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