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Yorodumi- EMDB-7792: Influenza hemagglutinin trimer plunged with a spot-to-plunge time... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7792 | |||||||||
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Title | Influenza hemagglutinin trimer plunged with a spot-to-plunge time of 100 ms | |||||||||
Map data | CryoSPARC auto-generated full map from the last refinement iteration. | |||||||||
Sample |
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Biological species | Influenza A virus (A/Hong Kong/26/1983(H3N2)) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.77 Å | |||||||||
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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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7792.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-7792-v30.xml emd-7792.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
Images | emd_7792.png | 68.5 KB | ||
Masks | emd_7792_msk_1.map | 64 MB | Mask map | |
Others | emd_7792_half_map_1.map.gz emd_7792_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7792 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7792 | HTTPS FTP |
-Validation report
Summary document | emd_7792_validation.pdf.gz | 79.3 KB | Display | EMDB validaton report |
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Full document | emd_7792_full_validation.pdf.gz | 78.4 KB | Display | |
Data in XML | emd_7792_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7792 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7792 | HTTPS FTP |
-Related structure data
Related structure data | 7623C 7624C 7625C 7627C 7628C 7629C 7630C 7788C 7791C C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10175 (Title: Single particle cryoEM of hemagglutinin with spot-to-plunge time of 100ms Data size: 288.3 Data #1: Full Leginon data collection, including all magnification images and aligned micrographs with and without dose weighting [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7792.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoSPARC auto-generated full map from the last refinement iteration. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8549 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_7792_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: CryoSPARC auto-generated half map from the last refinement iteration.
File | emd_7792_half_map_1.map | ||||||||||||
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Annotation | CryoSPARC auto-generated half map from the last refinement iteration. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoSPARC auto-generated mask from the last refinement iteration.
File | emd_7792_half_map_2.map | ||||||||||||
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Annotation | CryoSPARC auto-generated mask from the last refinement iteration. | ||||||||||||
Projections & Slices |
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Density Histograms |
-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: Influenza A virus (A/Hong Kong/26/1983(H3N2)) |
Recombinant expression | Organism: unidentified (others) |
Molecular weight | Experimental: 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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Grid | Model: Homemade |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER Details: 100 ms spot-to-plunge time. 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', ...Details: 100 ms spot-to-plunge time. 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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Corrected so that Cs is as close to 0 as possible. Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / 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 / Cs: 0.01 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |