+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20531 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Toll receptor EM map from template picks | ||||||||||||||||||||||||||||||
Map data | Sharpened map after CryoSparc 2.9 non-uniform refinement using template picks | ||||||||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.92 Å | ||||||||||||||||||||||||||||||
Authors | Rapp M / Bepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B | ||||||||||||||||||||||||||||||
Funding support | United States, 9 items
| ||||||||||||||||||||||||||||||
Citation | Journal: Nat Methods / Year: 2019 Title: Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Authors: Tristan Bepler / Andrew Morin / Micah Rapp / Julia Brasch / Lawrence Shapiro / Alex J Noble / Bonnie Berger / Abstract: Cryo-electron microscopy is a popular method for the determination of protein structures; however, identifying a sufficient number of particles for analysis can take months of manual effort. Current ...Cryo-electron microscopy is a popular method for the determination of protein structures; however, identifying a sufficient number of particles for analysis can take months of manual effort. Current computational approaches find many false positives and require ad hoc postprocessing, especially for unusually shaped particles. To address these shortcomings, we develop Topaz, an efficient and accurate particle-picking pipeline using neural networks trained with a general-purpose positive-unlabeled learning method. This framework enables particle detection models to be trained with few sparsely labeled particles and no labeled negatives. Topaz retrieves many more real particles than conventional picking methods while maintaining low false-positive rates, is capable of picking challenging unusually shaped proteins (for example, small, non-globular and asymmetric particles), produces more representative particle sets and does not require post hoc curation. We demonstrate the performance of Topaz on two difficult datasets and three conventional datasets. Topaz is modular, standalone, free and open source ( http://topaz.csail.mit.edu ). | ||||||||||||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20531.map.gz | 117.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-20531-v30.xml emd-20531.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
Images | emd_20531.png | 41.4 KB | ||
Masks | emd_20531_msk_1.map | 125 MB | Mask map | |
Others | emd_20531_additional.map.gz emd_20531_additional_1.map.gz emd_20531_half_map_1.map.gz emd_20531_half_map_2.map.gz | 62 MB 62 MB 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20531 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20531 | HTTPS FTP |
-Validation report
Summary document | emd_20531_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_20531_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_20531_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20531 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20531 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10215 (Title: Rabbit muscle aldolase single particle cryoEM / Data size: 1.4 TB Data #1: Micrographs along with all other magnification images from the collection [micrographs - single frame] Data #2: Micrograph frames [micrographs - multiframe] Data #3: CryoEM structures in the paper [picked particles - single frame - unprocessed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_20531.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map after CryoSparc 2.9 non-uniform refinement using template picks | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_20531_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened map after CryoSparc 2.9 non-uniform refinement using...
File | emd_20531_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened map after CryoSparc 2.9 non-uniform refinement using template picks | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened map after CryoSparc 2.9 non-uniform refinement using...
File | emd_20531_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened map after CryoSparc 2.9 non-uniform refinement using template picks | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map after CryoSparc 2.9 non-uniform refinement using...
File | emd_20531_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map after CryoSparc 2.9 non-uniform refinement using template picks | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map after CryoSparc 2.9 non-uniform refinement using...
File | emd_20531_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map after CryoSparc 2.9 non-uniform refinement using template picks | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Toll receptor
Entire | Name: Toll receptor |
---|---|
Components |
|
-Supramolecule #1: Toll receptor
Supramolecule | Name: Toll receptor / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) / Recombinant cell: S2 |
Molecular weight | Theoretical: 105 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
---|---|
Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Average electron dose: 73.48 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |