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Yorodumi- EMDB-1587: ab initio 3D reconstruction of GroEL using 3DESS (3D alignment by... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1587 | |||||||||
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Title | ab initio 3D reconstruction of GroEL using 3DESS (3D alignment by differential Evolution with Spectral Self-adaptation), which is a new high-resolution single-particle orientation refinement method based on spectrally self-adapting common lines | |||||||||
Map data | ab initio 3D reconstruction of GroEL using 3DESS | |||||||||
Sample |
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Keywords | GroEL / common lines / spectral self-adaptation | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
Authors | Elmlund D / Elmlund H | |||||||||
Citation | Journal: J Struct Biol / Year: 2009 Title: High-resolution single-particle orientation refinement based on spectrally self-adapting common lines. Authors: Dominika Elmlund / Hans Elmlund / Abstract: Three-dimensional (3D) structure determination from electron microscopic images of single molecules can be difficult for particles with low or no internal symmetry, and for images with low signal-to- ...Three-dimensional (3D) structure determination from electron microscopic images of single molecules can be difficult for particles with low or no internal symmetry, and for images with low signal-to-noise ratio (SNR), due to the existence of false maxima in the scoring function used for orientation search. In attempt to improve robustness of orientation parameter refinement towards noise and poor starting reconstruction quality, we have developed a method for common lines-based orientation search in Fourier space. The Fourier-space formulation enables inclusion of resolution (spatial frequency of the low-pass limit) as a variable that is adjusted in a particle-dependent, self-adaptive manner. The method allows for the underlying 3D structure to be estimated to high resolution, and requires only a crude, low-resolution reconstruction as starting-point for refinement. Benchmarking of the method is performed on experimental and synthetic data. | |||||||||
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_1587.map.gz | 10.1 MB | EMDB map data format | |
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Header (meta data) | emd-1587-v30.xml emd-1587.xml | 7.2 KB 7.2 KB | Display Display | EMDB header |
Images | 1587.gif | 78.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1587 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1587 | HTTPS FTP |
-Validation report
Summary document | emd_1587_validation.pdf.gz | 249.3 KB | Display | EMDB validaton report |
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Full document | emd_1587_full_validation.pdf.gz | 248.4 KB | Display | |
Data in XML | emd_1587_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1587 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1587 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1587.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ab initio 3D reconstruction of GroEL using 3DESS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.63 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 : GroEL data provided by National Resource for Automated Molecular ...
Entire | Name: GroEL data provided by National Resource for Automated Molecular Microscopy |
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Components |
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-Supramolecule #1000: GroEL data provided by National Resource for Automated Molecular ...
Supramolecule | Name: GroEL data provided by National Resource for Automated Molecular Microscopy type: sample / ID: 1000 Details: All sample details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39 Oligomeric state: 14-meric and d7 symmetric GroEL / Number unique components: 1 |
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-Supramolecule #1: GroEL
Supramolecule | Name: GroEL / type: organelle_or_cellular_component / ID: 1 / Name.synonym: GroEL / Recombinant expression: Yes |
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Source (natural) | 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
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Details | All imaging details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39 |
Image recording | Details: All image processing details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | All experimental details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39 |
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CTF correction | Details: each micrograph, phase flipping only |
Final reconstruction | Applied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Evol-Align |