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Yorodumi- EMDB-21373: Single particle reconstruction of HemQ from Geobacillus based on ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21373 | ||||||||||||||||||
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Title | Single particle reconstruction of HemQ from Geobacillus based on data acquired in the presence of substantial aberrations | ||||||||||||||||||
Map data | Single particle reconstruction of HemQ from Geobacillus based on data acquired in the presence of substantial aberrations | ||||||||||||||||||
Sample |
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Keywords | oxidoreductase / heme-binding | ||||||||||||||||||
Function / homology | Coproheme decarboxylase / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / heme biosynthetic process / peroxidase activity / heme binding / metal ion binding / Coproheme decarboxylase Function and homology information | ||||||||||||||||||
Biological species | Geobacillus sp. (strain Y412MC52) (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.32 Å | ||||||||||||||||||
Authors | Bromberg R / Guo Y | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: IUCrJ / Year: 2020 Title: High-resolution cryo-EM reconstructions in the presence of substantial aberrations. Authors: Raquel Bromberg / Yirui Guo / Dominika Borek / Zbyszek Otwinowski / Abstract: Here, an analysis is performed of how uncorrected antisymmetric aberrations, such as coma and trefoil, affect cryo-EM single-particle reconstruction (SPR) results, and an analytical formula ...Here, an analysis is performed of how uncorrected antisymmetric aberrations, such as coma and trefoil, affect cryo-EM single-particle reconstruction (SPR) results, and an analytical formula quantifying information loss owing to their presence is inferred that explains why Fourier-shell coefficient-based statistics may report significantly overestimated resolution if these aberrations are not fully corrected. The analysis is validated with reference-based aberration refinement for two cryo-EM SPR data sets acquired with a 200 kV microscope in the presence of coma exceeding 40 µm, and 2.3 and 2.7 Å reconstructions for 144 and 173 kDa particles, respectively, were obtained. The results provide a description of an efficient approach for assessing information loss in cryo-EM SPR data acquired in the presence of higher order aberrations, and address inconsistent guidelines regarding the level of aberrations that is acceptable in cryo-EM SPR experiments. #1: Journal: Biorxiv / Year: 2020 Title: High-resolution cryo-EM reconstructions in the presence of substantial aberrations Authors: Bromberg R / Guo Y / Borek D / Otwinowski Z | ||||||||||||||||||
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_21373.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-21373-v30.xml emd-21373.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_21373.png | 111.4 KB | ||
Filedesc metadata | emd-21373.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21373 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21373 | HTTPS FTP |
-Validation report
Summary document | emd_21373_validation.pdf.gz | 374.2 KB | Display | EMDB validaton report |
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Full document | emd_21373_full_validation.pdf.gz | 373.7 KB | Display | |
Data in XML | emd_21373_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_21373_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21373 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21373 | HTTPS FTP |
-Related structure data
Related structure data | 6vsaMC 6vrsC 6vscC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10363 (Title: 2.3 Angstrom cryo-EM reconstructions of HemQ from Geobacillus Data size: 1.4 TB Data #1: Unaligned multiframe data for 2.3 Angstrom cryo-EM reconstructions of HemQ from Geobacillus in the presence of substantial aberrations [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21373.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Single particle reconstruction of HemQ from Geobacillus based on data acquired in the presence of substantial aberrations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.72 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HemQ
Entire | Name: HemQ |
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Components |
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-Supramolecule #1: HemQ
Supramolecule | Name: HemQ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Geobacillus sp. (strain Y412MC52) (bacteria) |
Molecular weight | Theoretical: 144 KDa |
-Macromolecule #1: HemQ
Macromolecule | Name: HemQ / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO EC number: Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases |
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Source (natural) | Organism: Geobacillus sp. (strain Y412MC52) (bacteria) / Strain: Y412MC52 |
Molecular weight | Theoretical: 28.817609 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSEAAQTLDG WYCLHDFRTI DWSAWKTLPN EEREAAISEF LALVDQWETT ESEKQGSHAV YTIVGQKADI LFMILRPTLD ELHEIETAL NKTKLADYLL PAYSYVSVVE LSNYLASGSE DPYQIPEVRR RLYPILPKTN YICFYPMDKR RQGNDNWYML S MEQRRELM ...String: MSEAAQTLDG WYCLHDFRTI DWSAWKTLPN EEREAAISEF LALVDQWETT ESEKQGSHAV YTIVGQKADI LFMILRPTLD ELHEIETAL NKTKLADYLL PAYSYVSVVE LSNYLASGSE DPYQIPEVRR RLYPILPKTN YICFYPMDKR RQGNDNWYML S MEQRRELM RAHGMTGRKY AGKVTQIITG SVGLDDFEWG VTLFSDDALQ FKKLVYEMRF DEVSARFGEF GSFFVGTRLP ME NVSSFFH V UniProtKB: Coproheme decarboxylase |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 42 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 28 mg/mL |
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Buffer | pH: 7.5 / Component - Concentration: 20.0 mM / Component - Name: HEPES / Details: 100 mM NaCl |
Grid | Model: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS TALOS |
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Alignment procedure | Basic - Residual tilt: 6.9 mrad |
Details | The goal of the experiment was to show that it is possible to perform high resolution reconstruction in the presence of higher order aberrations. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-100 / Number grids imaged: 1 / Number real images: 268 / Average exposure time: 40.0 sec. / Average electron dose: 120.0 e/Å2 / Details: 258 movies were used in the reconstruction. |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | COOT was crucial as well. |
Refinement | Space: RECIPROCAL / Protocol: OTHER / Target criteria: REFMAC |
Output model | PDB-6vsa: |