+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1980 | |||||||||
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Title | CryoEM map of ParM filament at 7.2 Angstrom resolution | |||||||||
Map data | This is an volume file of parM filament | |||||||||
Sample |
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Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||
Authors | Gayathri P / Fujii T / Moller-Jensen J / van den Ent F / Namba K / Lowe J | |||||||||
Citation | Journal: Science / Year: 2012 Title: A bipolar spindle of antiparallel ParM filaments drives bacterial plasmid segregation. Authors: P Gayathri / T Fujii / J Møller-Jensen / F van den Ent / K Namba / J Löwe / Abstract: To ensure their stable inheritance by daughter cells during cell division, bacterial low-copy-number plasmids make simple DNA segregating machines that use an elongating protein filament between ...To ensure their stable inheritance by daughter cells during cell division, bacterial low-copy-number plasmids make simple DNA segregating machines that use an elongating protein filament between sister plasmids. In the ParMRC system of the Escherichia coli R1 plasmid, ParM, an actinlike protein, forms the spindle between ParRC complexes on sister plasmids. By using a combination of structural work and total internal reflection fluorescence microscopy, we show that ParRC bound and could accelerate growth at only one end of polar ParM filaments, mechanistically resembling eukaryotic formins. The architecture of ParM filaments enabled two ParRC-bound filaments to associate in an antiparallel orientation, forming a bipolar spindle. The spindle elongated as a bundle of at least two antiparallel filaments, thereby pushing two plasmid clusters toward the poles. | |||||||||
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_1980.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-1980-v30.xml emd-1980.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_1980.png | 170.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1980 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1980 | HTTPS FTP |
-Validation report
Summary document | emd_1980_validation.pdf.gz | 221.6 KB | Display | EMDB validaton report |
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Full document | emd_1980_full_validation.pdf.gz | 220.7 KB | Display | |
Data in XML | emd_1980_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1980 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1980 | HTTPS FTP |
-Related structure data
Related structure data | 4a6jMC 4a61C 4a62C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1980.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an volume file of parM filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.64 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 : ParM filament
Entire | Name: ParM filament |
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Components |
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-Supramolecule #1000: ParM filament
Supramolecule | Name: ParM filament / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: Plasmid segregation protein parM
Macromolecule | Name: Plasmid segregation protein parM / type: protein_or_peptide / ID: 1 / Name.synonym: parM / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 36 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | InterPro: Plasmid segregation protein ParM/StbA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 Details: 30 mM Tris-HCl, 25 mM KCl, 2 mM MgCl2, 1 mM DTT, pH 7.5 |
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Grid | Details: Quantifoil holey carbon molybdenum grid (R0.6/1.0, Quantifoil Micro Tools GmbH, Jena, Germany) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 50 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 3.5 seconds before plunging |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Min: 40 K / Max: 60 K / Average: 50 K |
Specialist optics | Energy filter - Name: Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV |
Date | Aug 17, 2009 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 207 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 91463 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal magnification: 50000 |
Sample stage | Specimen holder: top entry stage / Specimen holder model: JEOL |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 23.621 Å Applied symmetry - Helical parameters - Δ&Phi: 164.98 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER |
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CTF correction | Details: CTFFIND3 Each particle |