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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | ATP-bound IstB in complex to duplex DNA | |||||||||
![]() | Sharpened Map | |||||||||
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![]() | DNA Transposition / transposon / transpososome / AAA+ ATPases / target DNA / IS21 / IstB / Insertion sequence / DNA BINDING PROTEIN / cryo-electron microscopy. | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.18 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 | ![]() | 85.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.3 KB 27.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.2 KB | Display | ![]() |
Images | ![]() | 110.2 KB | ||
Masks | ![]() | 91.1 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() ![]() ![]() | 69.6 MB 2.5 MB 70 MB 70 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 905.9 KB | Display | ![]() |
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Full document | ![]() | 905.4 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8q3wMC ![]() 8q4dC M: atomic model generated by this map C: citing same article ( |
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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: 1.06 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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-Additional map: Unsharpened Map
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Annotation | Unsharpened Map | ||||||||||||
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-Additional map: Map used for modelling of amino-terminal domains after...
File | emd_18136_additional_2.map | ||||||||||||
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Annotation | Map used for modelling of amino-terminal domains after focused 3D classification | ||||||||||||
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-Half map: #1
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-Half map: #2
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Sample components
-Entire : IstB transposition regulator AAA+ ATPase bound to target DNA
Entire | Name: IstB transposition regulator AAA+ ATPase bound to target DNA |
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Components |
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-Supramolecule #1: IstB transposition regulator AAA+ ATPase bound to target DNA
Supramolecule | Name: IstB transposition regulator AAA+ ATPase bound to target DNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Complex of IstB transposition regulator AAA+ ATPase bound to target DNA |
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Molecular weight | Theoretical: 337 KDa |
-Supramolecule #2: Insertion sequence IS5376 putative ATP-binding protein
Supramolecule | Name: Insertion sequence IS5376 putative ATP-binding protein type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: DNA (48-MER) Target DNA FW and Rv
Supramolecule | Name: DNA (48-MER) Target DNA FW and Rv / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Insertion sequence IS5376 putative ATP-binding protein
Macromolecule | Name: Insertion sequence IS5376 putative ATP-binding protein type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 29.602275 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPNMKERIHE YCHRLHLPVM AERWSAMAEY ASTHNISYSE FLFRLLEAEI VEKQARSIQT LIKLSKLPYR KTIDTFDFTA QPSVDERRI RELLTLSFID RKENILFLGP PGIGKTHLAI SIGMEAIARG YKTYFITAHD LVNQLRRADQ EGKLEKKLRV F VKPTVLII ...String: GPNMKERIHE YCHRLHLPVM AERWSAMAEY ASTHNISYSE FLFRLLEAEI VEKQARSIQT LIKLSKLPYR KTIDTFDFTA QPSVDERRI RELLTLSFID RKENILFLGP PGIGKTHLAI SIGMEAIARG YKTYFITAHD LVNQLRRADQ EGKLEKKLRV F VKPTVLII DEMGYLKLDP NSAHYLFQVI ARRYEHAPII LTSNKSFGEW GEIVGDSVLA TAMLDRLLHH SIIFNLKGES YR LREKRLQ EEKQKDQ UniProtKB: Insertion sequence IS5376 putative ATP-binding protein |
-Macromolecule #2: DNA (48-MER) Target DNA FW
Macromolecule | Name: DNA (48-MER) Target DNA FW / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 18.401746 KDa |
Sequence | String: (DT)(DG)(DC)(DT)(DT)(DG)(DC)(DG)(DA)(DT) (DG)(DA)(DT)(DC)(DC)(DG)(DA)(DC)(DG)(DT) (DG)(DT)(DT)(DA)(DG)(DC)(DC)(DA)(DC) (DG)(DC)(DT)(DG)(DA)(DC)(DT)(DA)(DG)(DT) (DT) (DA)(DT)(DG)(DC)(DC)(DA) ...String: (DT)(DG)(DC)(DT)(DT)(DG)(DC)(DG)(DA)(DT) (DG)(DA)(DT)(DC)(DC)(DG)(DA)(DC)(DG)(DT) (DG)(DT)(DT)(DA)(DG)(DC)(DC)(DA)(DC) (DG)(DC)(DT)(DG)(DA)(DC)(DT)(DA)(DG)(DT) (DT) (DA)(DT)(DG)(DC)(DC)(DA)(DT)(DG) (DC)(DC)(DT)(DC)(DC)(DC)(DT)(DT)(DC)(DA) (DG)(DG) |
-Macromolecule #3: DNA (48-MER) Traget DNA Rv
Macromolecule | Name: DNA (48-MER) Traget DNA Rv / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 18.584918 KDa |
Sequence | String: (DC)(DC)(DT)(DG)(DA)(DA)(DG)(DG)(DG)(DA) (DG)(DG)(DC)(DA)(DT)(DG)(DG)(DC)(DA)(DT) (DA)(DA)(DC)(DT)(DA)(DG)(DT)(DC)(DA) (DG)(DC)(DG)(DT)(DG)(DG)(DC)(DT)(DA)(DA) (DC) (DA)(DC)(DG)(DT)(DC)(DG) ...String: (DC)(DC)(DT)(DG)(DA)(DA)(DG)(DG)(DG)(DA) (DG)(DG)(DC)(DA)(DT)(DG)(DG)(DC)(DA)(DT) (DA)(DA)(DC)(DT)(DA)(DG)(DT)(DC)(DA) (DG)(DC)(DG)(DT)(DG)(DG)(DC)(DT)(DA)(DA) (DC) (DA)(DC)(DG)(DT)(DC)(DG)(DG)(DA) (DT)(DC)(DA)(DT)(DC)(DG)(DC)(DA)(DA)(DG) (DC)(DA) |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 10 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 10 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-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: 5.0 sec. / Average electron dose: 60.0 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: 1.2 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: 95.21 |
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Output model | ![]() PDB-8q3w: |