+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6314 | |||||||||
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Title | Catalase solved at 3.2 Angstrom resolution by MicroED | |||||||||
Map data | Catalase diffraction data phased by molecular replacement | |||||||||
Sample |
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Keywords | catalase / microcrystal | |||||||||
Function / homology | Function and homology information catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / peroxisomal matrix / positive regulation of cell division / hydrogen peroxide catabolic process ...catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / peroxisomal matrix / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / enzyme binding / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Nannenga BL / Shi D / Hattne J / Reyes FE / Gonen T | |||||||||
Citation | Journal: Elife / Year: 2014 Title: Structure of catalase determined by MicroED. Authors: Brent L Nannenga / Dan Shi / Johan Hattne / Francis E Reyes / Tamir Gonen / Abstract: MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of ...MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. | |||||||||
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_6314.map.gz | 16.5 MB | EMDB map data format | |
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Header (meta data) | emd-6314-v30.xml emd-6314.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | 400_6314.gif 80_6314.gif | 105.4 KB 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6314 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6314 | HTTPS FTP |
-Validation report
Summary document | emd_6314_validation.pdf.gz | 392 KB | Display | EMDB validaton report |
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Full document | emd_6314_full_validation.pdf.gz | 391.6 KB | Display | |
Data in XML | emd_6314_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6314 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6314 | HTTPS FTP |
-Related structure data
Related structure data | 3j7bMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6314.map.gz / Format: CCP4 / Size: 17.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Catalase diffraction data phased by molecular replacement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.75156 Å / Y: 0.79667 Å / Z: 0.75863 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : catalase
Entire | Name: catalase |
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Components |
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-Supramolecule #1000: catalase
Supramolecule | Name: catalase / type: sample / ID: 1000 / Details: catalase microcrystals / Oligomeric state: tetramer / Number unique components: 1 |
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Molecular weight | Theoretical: 240 KDa |
-Macromolecule #1: catalase
Macromolecule | Name: catalase / type: protein_or_peptide / ID: 1 / Details: catalase microcrystals / Oligomeric state: tetramer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: bovine / Tissue: liver |
Molecular weight | Theoretical: 240 KDa |
Sequence | UniProtKB: Catalase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 6.3 / Details: 50 mM sodium phosphate |
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Grid | Details: 300 mesh copper grid with holey carbon support |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV Method: Crystals were added to the grid for 30 seconds and then blotted for 2 to 6 seconds. |
Details | Catalase containing 10% sodium chloride was dialyzed overnight in 50 mM sodium phosphate to remove the sodium chloride. Crystals formed following dialysis. |
Crystal formation | Details: Catalase containing 10% sodium chloride was dialyzed overnight in 50 mM sodium phosphate to remove the sodium chloride. Crystals formed following dialysis. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 90 K / Max: 110 K / Average: 100 K |
Date | Jun 15, 2014 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.1 e/Å2 / Camera length: 2000 Details: Raw diffraction images are available upon request. Contact the Gonen lab for access. |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle min: -55 / Tilt angle max: 55 / Tilt series - Axis1 - Min angle: -55 ° / Tilt series - Axis1 - Max angle: 55 ° |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
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Crystal parameters | Unit cell - A: 67.84 Å / Unit cell - B: 172.08 Å / Unit cell - C: 182.070 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 21 21 21 |