+Open data
-Basic information
Entry | Database: PDB / ID: 5ai7 | ||||||
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Title | ParM doublet model | ||||||
Components | PLASMID SEGREGATION PROTEIN PARM | ||||||
Keywords | MOTOR PROTEIN / PARM / ACTIN-LIKE PROTEIN / DOUBLET / ANTIPARALLEL | ||||||
Function / homology | Plasmid segregation protein ParM/StbA / : / Plasmid segregation protein ParM, N-terminal / Plasmid segregation protein ParM, C-terminal / ParM-like / plasmid partitioning / ATPase, nucleotide binding domain / identical protein binding / Plasmid segregation protein ParM Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K, L, M, N | ||||||
Authors | Bharat, T.A.M. / Murshudov, G.N. / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ai7.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ai7.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ai7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ai7_validation.pdf.gz | 622.9 KB | Display | wwPDB validaton report |
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Full document | 5ai7_full_validation.pdf.gz | 625.4 KB | Display | |
Data in XML | 5ai7_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 5ai7_validation.cif.gz | 68.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/5ai7 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/5ai7 | HTTPS FTP |
-Related structure data
Related structure data | 2848MC 2849C 2850C 5aeyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 35633.223 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Details: THIS IS A MODEL OF THE PARM DOUBLET BASED ON CRYO-EM DATA. ONLY CARBON-ALPHAS HAVE BEEN DEPOSITED. Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: P11904 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: PARM ANTIPARALLEL DOUBLET / Type: COMPLEX |
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Buffer solution | Name: 50 MM TRIS-HCL, 100 MM KCL, AND 1 MM MGCL2, 2% PEG 6000 pH: 7 Details: 50 MM TRIS-HCL, 100 MM KCL, AND 1 MM MGCL2, 2% PEG 6000 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Details: VIROBOT MARK IV (FEI) |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 3000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 0.3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software | Name: SPRING / Category: 3D reconstruction / Details: SPRING (DESFOSSES AND SACHSE) | ||||||||||||
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3D reconstruction | Method: CRYO-EM ALIGNMENT Details: THIS IS A MODEL OF THE PARM ANTIPARALLEL ANTIPARALLEL DOUBLET BASED ON CRYOEM DATA. TWO COPIES OF THE PARM AMPPNP CRYO-EM FILAMENT STRUCTURE WERE PLACED IN AN ANTIPARALLEL ORIENTATION. ...Details: THIS IS A MODEL OF THE PARM ANTIPARALLEL ANTIPARALLEL DOUBLET BASED ON CRYOEM DATA. TWO COPIES OF THE PARM AMPPNP CRYO-EM FILAMENT STRUCTURE WERE PLACED IN AN ANTIPARALLEL ORIENTATION. ANTIPARALLEL ASSIGNMENT WAS DONE USING CRYO-EM ALIGNMENT. THIS IS A MODEL OF THE PARM ANTIPARALLEL DOUBLET CONSTRUCTED USING CRYO-EM DATA. ONLY C-ALPHAS HAVE BEEN DEPOSITED. Symmetry type: HELICAL | ||||||||||||
Refinement step | Cycle: LAST
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