+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25764 | ||||||||||||
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Title | human DNA polymerase gamma accessory subunit, POLG2 | ||||||||||||
Map data | human DNA polymerase gamma accessory subunit, POLG2 | ||||||||||||
Sample |
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Keywords | processivity factor / accessory subunit / DNA BINDING PROTEIN | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Riccio AA / Bouvette J / Borgnia MJ / Copeland WC | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Elife / Year: 2022 Title: Automated systematic evaluation of cryo-EM specimens with SmartScope. Authors: Jonathan Bouvette / Qinwen Huang / Amanda A Riccio / William C Copeland / Alberto Bartesaghi / Mario J Borgnia / Abstract: Finding the conditions to stabilize a macromolecular target for imaging remains the most critical barrier to determining its structure by cryo-electron microscopy (cryo-EM). While automation has ...Finding the conditions to stabilize a macromolecular target for imaging remains the most critical barrier to determining its structure by cryo-electron microscopy (cryo-EM). While automation has significantly increased the speed of data collection, specimens are still screened manually, a laborious and subjective task that often determines the success of a project. Here, we present SmartScope, the first framework to streamline, standardize, and automate specimen evaluation in cryo-EM. SmartScope employs deep-learning-based object detection to identify and classify features suitable for imaging, allowing it to perform thorough specimen screening in a fully automated manner. A web interface provides remote control over the automated operation of the microscope in real time and access to images and annotation tools. Manual annotations can be used to re-train the feature recognition models, leading to improvements in performance. Our automated tool for systematic evaluation of specimens streamlines structure determination and lowers the barrier of adoption for cryo-EM. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25764.map.gz | 56.8 MB | EMDB map data format | |
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Header (meta data) | emd-25764-v30.xml emd-25764.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25764_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_25764.png | 162.2 KB | ||
Filedesc metadata | emd-25764.cif.gz | 4.9 KB | ||
Others | emd_25764_half_map_1.map.gz emd_25764_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25764 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25764 | HTTPS FTP |
-Validation report
Summary document | emd_25764_validation.pdf.gz | 727.5 KB | Display | EMDB validaton report |
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Full document | emd_25764_full_validation.pdf.gz | 727 KB | Display | |
Data in XML | emd_25764_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_25764_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25764 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25764 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25764.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | human DNA polymerase gamma accessory subunit, POLG2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 2
File | emd_25764_half_map_1.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 1
File | emd_25764_half_map_2.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human DNA polymerase gamma accessory subunit, POLG2
Entire | Name: human DNA polymerase gamma accessory subunit, POLG2 |
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Components |
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-Supramolecule #1: human DNA polymerase gamma accessory subunit, POLG2
Supramolecule | Name: human DNA polymerase gamma accessory subunit, POLG2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54 KDa |
-Macromolecule #1: human DNA polymerase gamma accessory subunit, POLG2
Macromolecule | Name: human DNA polymerase gamma accessory subunit, POLG2 / type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MRGSHHHHHH GSTMDAGQPE LLTERSSPKG GHVKSHAELE GNGEHPEAPG SGEG SEALL EICQRRHFLS GSKQQLSRDS LLSGCHPGFG PLGVELRKNL AAEWWTSVVV FREQVFPVDA LHHKPGPLLP GDSAFRLVSA ETLREILQDK ELSKEQLVTF LENVLKTSGK ...String: MRGSHHHHHH GSTMDAGQPE LLTERSSPKG GHVKSHAELE GNGEHPEAPG SGEG SEALL EICQRRHFLS GSKQQLSRDS LLSGCHPGFG PLGVELRKNL AAEWWTSVVV FREQVFPVDA LHHKPGPLLP GDSAFRLVSA ETLREILQDK ELSKEQLVTF LENVLKTSGK LRENLLHGAL EHYVNCLDLV NKRLPYGLAQ IGVCFHPVFD TKQIRNGVKS IGEKTEASLV WFTPPRTSNQ WLDFWLRHRL QWWRKFAMSP SNFSSSDCQD EEGRKGNKLY YNFPWGKELI ETLWNLGDHE LLHMYPGNVS KLHGRDGRKN VVPCVLSVNG DLDRGMLAYL YDSFQLTENS FTRKKNLHRK VLKLHPCLAP IKVALDVGRG PTLELRQVCQ GLFNELLENG ISVWPGYLET MQSSLEQLYS KYDEMSILFT VLVTETTLEN GLIHLRSRDT TMKEMMHISK LKDFLIKYIS SAKNV |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.22 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3838 pixel / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |