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Yorodumi- EMDB-7791: Insulin Receptor ectodomain in complex with two insulin molecules... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7791 | |||||||||
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Title | Insulin Receptor ectodomain in complex with two insulin molecules plunged with a spot-to-plunge time of 800 ms | |||||||||
Map data | CryoSPARC auto-generated sharpened map from last iteration of refinement. | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.09 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_7791.map.gz | 85.3 MB | EMDB map data format | |
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Header (meta data) | emd-7791-v30.xml emd-7791.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_7791.png | 62.1 KB | ||
Masks | emd_7791_msk_1.map | 91.1 MB | Mask map | |
Others | emd_7791_half_map_1.map.gz emd_7791_half_map_2.map.gz | 84.4 MB 84.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7791 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7791 | HTTPS FTP |
-Validation report
Summary document | emd_7791_validation.pdf.gz | 79 KB | Display | EMDB validaton report |
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Full document | emd_7791_full_validation.pdf.gz | 78.1 KB | Display | |
Data in XML | emd_7791_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7791 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7791 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7791.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoSPARC auto-generated sharpened map from last iteration of refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 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_7791_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: CryoSPARC auto-generated half-map from last iteration of refinement.
File | emd_7791_half_map_1.map | ||||||||||||
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Annotation | CryoSPARC auto-generated half-map from last iteration of refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoSPARC auto-generated half-map from last iteration of refinement.
File | emd_7791_half_map_2.map | ||||||||||||
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Annotation | CryoSPARC auto-generated half-map from last iteration of refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Insulin Receptor Ectodomain in complex with two insulin molecules
Entire | Name: Insulin Receptor Ectodomain in complex with two insulin molecules |
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Components |
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-Supramolecule #1: Insulin Receptor Ectodomain in complex with two insulin molecules
Supramolecule | Name: Insulin Receptor Ectodomain in complex with two insulin molecules type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Ovis aries (sheep) |
Molecular weight | Experimental: 215 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Homemade |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER Details: 800 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: 800 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: 66.0 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 magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |