+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10402 | |||||||||
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Title | Stalled FtsK motor domain bound to dsDNA end | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA translocation / DNA motor / RecA fold / Divisome / DNA BINDING PROTEIN | |||||||||
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 (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) / synthetic construct (others) / Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.99 Å | |||||||||
Authors | Jean NL / Lowe J | |||||||||
Funding support | United Kingdom, 2 items
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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 NL / Rutherford TJ / Lowe J | |||||||||
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_10402.map.gz | 5.8 MB | EMDB map data format | |
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Header (meta data) | emd-10402-v30.xml emd-10402.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10402_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_10402.png | 162.1 KB | ||
Filedesc metadata | emd-10402.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10402 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10402 | HTTPS FTP |
-Validation report
Summary document | emd_10402_validation.pdf.gz | 426.7 KB | Display | EMDB validaton report |
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Full document | emd_10402_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | emd_10402_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_10402_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10402 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10402 | HTTPS FTP |
-Related structure data
Related structure data | 6t8oMC 6t8bC 6t8gC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10402.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 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 : FtsK motor domain at dsDNA end, stalled state
Entire | Name: FtsK motor domain at dsDNA end, stalled state |
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Components |
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-Supramolecule #1: FtsK motor domain at dsDNA end, stalled state
Supramolecule | Name: FtsK motor domain at dsDNA end, stalled state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: FtsK motor domain
Supramolecule | Name: FtsK motor domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: DNA translocase FtsK
Macromolecule | Name: DNA translocase FtsK / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
Molecular weight | Theoretical: 54.001441 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVPDRREQSK AKERLLEREE ALAKHMSERE KRPPPKIDPP PSPKAPEPSK RVLKEKQAPL FVDTAVEGTL PPLSLLDPAE VKQKSYSPE SLEAMSRLLE IKLKEFGVEV SVDSVHPGPV ITRFEIQPAA GVKVSRISNL AKDLARSLAV ISVRVVEVIP G KTTVGIEI ...String: MVPDRREQSK AKERLLEREE ALAKHMSERE KRPPPKIDPP PSPKAPEPSK RVLKEKQAPL FVDTAVEGTL PPLSLLDPAE VKQKSYSPE SLEAMSRLLE IKLKEFGVEV SVDSVHPGPV ITRFEIQPAA GVKVSRISNL AKDLARSLAV ISVRVVEVIP G KTTVGIEI PNEDRQMVRF SEVLSSPEYD EHKSTVPLAL GHDIGGRPII TDLAKMPHLL VAGTTGSGKS VGVNAMLLSI LF KSTPSEA RLIMIDPKML ELSIYEGIPH LLCPVVTDMK EAANALRWSV AEMERRYRLM AAMGVRNLAG FNRKVKDAEE AGT PLTDPL FRRESPDDEP PQLSTLPTIV VVVDEFADMM MIVGKKVEEL IARIAQKARA AGIHLILATQ RPSVDVITGL IKAN IPTRI AFQVSSKIDS RTILDQGGAE QLLGHGDMLY LPPGTGLPIR VHGAFVSDDE VHRVVEAWKL RGAPDYIEDI LAGVD EGGK LHHHHHH UniProtKB: DNA translocase FtsK |
-Macromolecule #2: dsDNA substrate
Macromolecule | Name: dsDNA substrate / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 4.276839 KDa |
Sequence | String: (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT) |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||
Details | 0.7 m/mL FtsK 1.5 uM 45 bp DNA |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 3300 / Average electron dose: 42.95 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |