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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | IstA-IstB(E167Q) Strand Transfer Complex | |||||||||
![]() | sharpened map | |||||||||
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![]() | DNA transposition / DNA integration / transposon / transpososome / holo-transpososome / insertion sequence / IS21 / IstA / IstB / DDE transposase / DDE domain / AAA+ ATPase / DNA strand transfer complex / STC / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() transposition / DNA strand exchange activity / DNA integration / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.62 Å | |||||||||
![]() | de la Gandara A / Spinola-Amilibia M / Araujo-Bazan L / Nunez-Ramirez R / Berger JM / Arias-Palomo E | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for transposase activation by a dedicated AAA+ ATPase. Authors: Álvaro de la Gándara / Mercedes Spínola-Amilibia / Lidia Araújo-Bazán / Rafael Núñez-Ramírez / James M Berger / Ernesto Arias-Palomo / ![]() ![]() Abstract: Transposases drive chromosomal rearrangements and the dissemination of drug-resistance genes and toxins. Although some transposases act alone, many rely on dedicated AAA+ ATPase subunits that ...Transposases drive chromosomal rearrangements and the dissemination of drug-resistance genes and toxins. Although some transposases act alone, many rely on dedicated AAA+ ATPase subunits that regulate site selectivity and catalytic function through poorly understood mechanisms. Using IS21 as a model transposase system, we show how an ATPase regulator uses nucleotide-controlled assembly and DNA deformation to enable structure-based site selectivity, transposase recruitment, and activation and integration. Solution and cryogenic electron microscopy studies show that the IstB ATPase self-assembles into an autoinhibited pentamer of dimers that tightly curves target DNA into a half-coil. Two of these decamers dimerize, which stabilizes the target nucleic acid into a kinked S-shaped configuration that engages the IstA transposase at the interface between the two IstB oligomers to form an approximately 1 MDa transpososome complex. Specific interactions stimulate regulator ATPase activity and trigger a large conformational change on the transposase that positions the catalytic site to perform DNA strand transfer. These studies help explain how AAA+ ATPase regulators-which are used by classical transposition systems such as Tn7, Mu and CRISPR-associated elements-can remodel their substrate DNA and cognate transposases to promote function. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 347.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.3 KB 31.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.3 KB | Display | ![]() |
Images | ![]() | 136.1 KB | ||
Masks | ![]() | 371.3 MB | ![]() | |
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() ![]() ![]() | 347.3 MB 295 MB 294.9 MB 294.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 957.6 KB | Display | ![]() |
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Full document | ![]() | 957.2 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8q4dMC ![]() 18136 ![]() 8q3wC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.98498 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
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Sample components
+Entire : IstA-IstB(E167Q) Strand Transfer Complex
+Supramolecule #1: IstA-IstB(E167Q) Strand Transfer Complex
+Supramolecule #2: IstA-IstB(E167Q) Strand
+Supramolecule #3: DNA
+Macromolecule #1: Putative transposase for insertion sequence element IS5376
+Macromolecule #2: Insertion sequence IS5376 putative ATP-binding protein
+Macromolecule #3: DNA (118-MER) / TIR-transferred strand
+Macromolecule #4: DNA (58-MER) / TIR non-transferred strand
+Macromolecule #5: DNA (58-MER) / target-reverse complement
+Macromolecule #6: MAGNESIUM ION
+Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.1 sec. / Average electron dose: 51.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 91.21 |
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Output model | ![]() PDB-8q4d: |