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Yorodumi- EMDB-3810: Tomogram of e. coli carrying empty ple6 plasmid induced with 20 u... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3810 | |||||||||
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Title | Tomogram of e. coli carrying empty ple6 plasmid induced with 20 uM IPTG | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Swulius MT / Jensen GJ | |||||||||
Citation | Journal: J Bacteriol / Year: 2012 Title: The helical MreB cytoskeleton in Escherichia coli MC1000/pLE7 is an artifact of the N-Terminal yellow fluorescent protein tag. Authors: Matthew T Swulius / Grant J Jensen / Abstract: Based on fluorescence microscopy, the actin homolog MreB has been thought to form extended helices surrounding the cytoplasm of rod-shaped bacterial cells. The presence of these and other putative ...Based on fluorescence microscopy, the actin homolog MreB has been thought to form extended helices surrounding the cytoplasm of rod-shaped bacterial cells. The presence of these and other putative helices has come to dominate models of bacterial cell shape regulation, chromosome segregation, polarity, and motility. Here we use electron cryotomography to show that MreB does in fact form extended helices and filaments in Escherichia coli when yellow fluorescent protein (YFP) is fused to its N terminus but native (untagged) MreB expressed to the same levels does not. In contrast, mCherry fused to an internal loop (MreB-RFP(SW)) does not induce helices. The helices are therefore an artifact of the placement of the fluorescent protein tag. YFP-MreB helices were also clearly distinguishable from the punctate, "patchy" localization patterns of MreB-RFP(SW), even by standard light microscopy. The many interpretations in the literature of such punctate patterns as helices should therefore be reconsidered. | |||||||||
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_3810.map.gz | 587.9 MB | EMDB map data format | |
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Header (meta data) | emd-3810-v30.xml emd-3810.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_3810.png | 136 KB | ||
Others | emd_3810_additional_1.map.gz emd_3810_additional_2.map.gz emd_3810_additional_3.map.gz | 633.6 MB 630.3 MB 643.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3810 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3810 | HTTPS FTP |
-Validation report
Summary document | emd_3810_validation.pdf.gz | 183.8 KB | Display | EMDB validaton report |
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Full document | emd_3810_full_validation.pdf.gz | 182.9 KB | Display | |
Data in XML | emd_3810_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3810 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3810 | HTTPS FTP |
-Related structure data
Related structure data | 3811C 3812C C: citing same article (ref.) |
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EM raw data | EMPIAR-10113 (Title: Tilt-series of e. coli carrying empty ple6 plasmid induced with 20 uM IPTG Data size: 3.8 Data #1: Tilt-series of the E. coli carrying empty ple6 plasmid induced with 20 uM IPTG [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3810.map.gz / Format: CCP4 / Size: 984.4 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 9.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_3810_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_3810_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #3
File | emd_3810_additional_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Escherichia Coli
Entire | Name: Escherichia Coli (E. coli) |
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Components |
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-Supramolecule #1: Escherichia Coli
Supramolecule | Name: Escherichia Coli / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Supramolecule #2: Helical MreB Cytoskeleton
Supramolecule | Name: Helical MreB Cytoskeleton / type: organelle_or_cellular_component / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 / Component - Concentration: 50.0 ug/ml / Component - Formula: C16H19N3O4S / Component - Name: Ampicillin Details: MC1000, MC1000/pLE6, and MC1000/pLE7 were grown in LB at 37C with 50 ug/ml ampicillin when appropriate. |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Max: 123.15 K |
Specialist optics | Energy filter - Name: FEI |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 1016 pixel / Digitization - Dimensions - Height: 1016 pixel / Average electron dose: 0.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: IMOD Software - details: Tomograms were reconstructed and modelled Number images used: 501 |
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