+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2849 | |||||||||
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Title | E coli cell with plasmid containing the ParMRC locus | |||||||||
Map data | E coli cell with plasmid containing the ParMRC locus | |||||||||
Sample |
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Keywords | bacterial cytoskeleton / plasmid segregation / actin-like protein | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Bharat TAM / Murshudov GN / Sachse C / Lowe J | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles. Authors: Tanmay A M Bharat / Garib N Murshudov / Carsten Sachse / Jan Löwe / Abstract: Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with ...Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation. | |||||||||
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_2849.map.gz | 625.8 MB | EMDB map data format | |
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Header (meta data) | emd-2849-v30.xml emd-2849.xml | 8.1 KB 8.1 KB | Display Display | EMDB header |
Images | emd-2849.png | 431.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2849 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2849 | HTTPS FTP |
-Validation report
Summary document | emd_2849_validation.pdf.gz | 146.9 KB | Display | EMDB validaton report |
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Full document | emd_2849_full_validation.pdf.gz | 146.1 KB | Display | |
Data in XML | emd_2849_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2849 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2849 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2849.map.gz / Format: CCP4 / Size: 665.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E coli cell with plasmid containing the ParMRC locus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 17.8 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 : E coli cell with plasmid containing medium copy number plasmid wi...
Entire | Name: E coli cell with plasmid containing medium copy number plasmid with ParMRC locus |
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Components |
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-Supramolecule #1000: E coli cell with plasmid containing medium copy number plasmid wi...
Supramolecule | Name: E coli cell with plasmid containing medium copy number plasmid with ParMRC locus type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Escherichia coli cytoskeleton
Supramolecule | Name: Escherichia coli cytoskeleton / type: organelle_or_cellular_component / ID: 1 / Details: 200 mesh copper / rhodium grid with carbon support / Recombinant expression: No / Database: NCBI |
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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
Grid | Details: 200 mesh copper / rhodium grid with carbon support |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: Gatan Quantum Energy Filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Jun 1, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 121 / Average electron dose: 120 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -8.0 µm / Nominal defocus min: -8.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Angle increment: 1 ° |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Tilt series was aligned using IMOD and reconstructed using Tomo3D |
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Final reconstruction | Algorithm: OTHER / Software - Name: IMOD, Tomo3D / Number images used: 121 |