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Open data
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Basic information
Entry | Database: PDB / ID: 4a6j | ||||||
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Title | Structural model of ParM filament based on CryoEM map | ||||||
![]() | PLASMID SEGREGATION PROTEIN PARM | ||||||
![]() | TRANSPORT PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å | ||||||
![]() | Gayathri, P. / Fujii, T. / Moller-Jensen, J. / Van Den Ent, F. / Namba, K. / Lowe, J. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 620 KB | Display | ![]() |
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PDB format | ![]() | 509.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 106.5 KB | Display | |
Data in CIF | ![]() | 133.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1980MC ![]() 4a61C ![]() 4a62C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 35804.375 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ANP / #3: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: PARM FILAMENT / Type: COMPLEX |
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Buffer solution | Name: 30 MM TRIS-HCL, 25 MM KCL, 2 MM MGCL2, 1 MM DTT, 5MM AMPPNP pH: 7.5 Details: 30 MM TRIS-HCL, 25 MM KCL, 2 MM MGCL2, 1 MM DTT, 5MM AMPPNP |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHENE |
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Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC / Date: Aug 17, 2009 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 91463 X / Cs: 1.6 mm |
Specimen holder | Temperature: 50 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
Image scans | Num. digital images: 207 |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: CTFFIND3 EACH PARTICLE | ||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 7.2 Å / Actual pixel size: 1.64 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMD-1980. (DEPOSITION ID: 10363). Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY | ||||||||||||
Atomic model building | PDB-ID: 4A62 Accession code: 4A62 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 7.2 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.2 Å
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