+Open data
-Basic information
Entry | Database: PDB / ID: 6t8b | |||||||||
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Title | FtsK motor domain with dsDNA, translocating state | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA translocation / DNA motor / RecA fold / Divisome | |||||||||
Function / homology | Function and homology information cellular response to antibiotic / chromosome segregation / cell division / DNA binding / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å | |||||||||
Authors | Jean, N.L. / Lowe, J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: FtsK in motion reveals its mechanism for double-stranded DNA translocation. Authors: Nicolas L Jean / Trevor J Rutherford / Jan Löwe / Abstract: FtsK protein contains a fast DNA motor that is involved in bacterial chromosome dimer resolution. During cell division, FtsK translocates double-stranded DNA until both recombination sites are ...FtsK protein contains a fast DNA motor that is involved in bacterial chromosome dimer resolution. During cell division, FtsK translocates double-stranded DNA until both recombination sites are placed at mid cell for subsequent dimer resolution. Here, we solved the 3.6-Å resolution electron cryo-microscopy structure of the motor domain of FtsK while translocating on its DNA substrate. Each subunit of the homo-hexameric ring adopts a unique conformation and one of three nucleotide states. Two DNA-binding loops within four subunits form a pair of spiral staircases within the ring, interacting with the two DNA strands. This suggests that simultaneous conformational changes in all ATPase domains at each catalytic step generate movement through a mechanism related to filament treadmilling. While the ring is only rotating around the DNA slowly, it is instead the conformational states that rotate around the ring as the DNA substrate is pushed through. #1: Journal: Biorxiv Title: FtsK in motion reveals its mechanism for double-stranded DNA translocation Authors: Jean, N.L. / Rutherford, T.J. / Lowe, J. | |||||||||
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 | 6t8b.cif.gz | 431.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t8b.ent.gz | 346 KB | Display | PDB format |
PDBx/mmJSON format | 6t8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t8b_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6t8b_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6t8b_validation.xml.gz | 75 KB | Display | |
Data in CIF | 6t8b_validation.cif.gz | 111.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/6t8b ftp://data.pdbj.org/pub/pdb/validation_reports/t8/6t8b | HTTPS FTP |
-Related structure data
Related structure data | 10399MC 6t8gC 6t8oC 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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1 |
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-Components
#1: Protein | Mass: 54001.441 Da / Num. of mol.: 6 / Fragment: Motor domain, residues 247-728 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: ftsK, PA2615 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9I0M3 #2: DNA chain | Mass: 6129.039 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Sequence not determined due to sequence heterogeneity of the protein-bound DNA Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.7 m/mL FtsK 1.5 uM 45 bp DNA | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 |
Image recording | Electron dose: 42.95 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3300 |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56485 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2IUU Pdb chain-ID: A / Accession code: 2IUU / Source name: PDB / Type: experimental model |