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Yorodumi- EMDB-40222: CryoEM structure of the TnsC(1-503)-TnsD(1-318)-DNA complex in a ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40222 | |||||||||
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Title | CryoEM structure of the TnsC(1-503)-TnsD(1-318)-DNA complex in a 6:2:1 stoichiometry from E. coli Tn7 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Transposon / AAA+ ATPase / Oligomer / Complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information transposition / DNA recombination / ATP hydrolysis activity / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.88 Å | |||||||||
Authors | Shen Y / Guarne A | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Assembly of the Tn7 targeting complex by a regulated stepwise process. Authors: Yao Shen / Shreya S Krishnan / Michael T Petassi / Mark A Hancock / Joseph E Peters / Alba Guarné / Abstract: The Tn7 family of transposons is notable for its highly regulated integration mechanisms, including programmable RNA-guided transposition. The targeting pathways rely on dedicated target selection ...The Tn7 family of transposons is notable for its highly regulated integration mechanisms, including programmable RNA-guided transposition. The targeting pathways rely on dedicated target selection proteins from the TniQ family and the AAA+ adaptor TnsC to recruit and activate the transposase at specific target sites. Here, we report the cryoelectron microscopy (cryo-EM) structures of TnsC bound to the TniQ domain of TnsD from prototypical Tn7 and unveil key regulatory steps stemming from unique behaviors of ATP- versus ADP-bound TnsC. We show that TnsD recruits ADP-bound dimers of TnsC and acts as an exchange factor to release one protomer with exchange to ATP. This loading process explains how TnsC assembles a heptameric ring unidirectionally from the target site. This unique loading process results in functionally distinct TnsC protomers within the ring, providing a checkpoint for target immunity and explaining how insertions at programmed sites precisely occur in a specific orientation across Tn7 elements. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40222.map.gz | 225.3 MB | EMDB map data format | |
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Header (meta data) | emd-40222-v30.xml emd-40222.xml | 25.5 KB 25.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40222_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_40222.png | 144.6 KB | ||
Filedesc metadata | emd-40222.cif.gz | 6.8 KB | ||
Others | emd_40222_additional_1.map.gz emd_40222_additional_2.map.gz emd_40222_half_map_1.map.gz emd_40222_half_map_2.map.gz | 230 MB 124.8 MB 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40222 | HTTPS FTP |
-Validation report
Summary document | emd_40222_validation.pdf.gz | 833.3 KB | Display | EMDB validaton report |
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Full document | emd_40222_full_validation.pdf.gz | 832.9 KB | Display | |
Data in XML | emd_40222_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | emd_40222_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40222 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40222 | HTTPS FTP |
-Related structure data
Related structure data | 8glxMC 8gluC 8glwC 8vcjC 8vctC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40222.map.gz / Format: CCP4 / Size: 244.1 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: 0.855 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_40222_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: #2
File | emd_40222_additional_2.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_40222_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40222_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of TnsC(1-503) bound to TnsD(1-318) and DNA with cofactor...
+Supramolecule #1: Complex of TnsC(1-503) bound to TnsD(1-318) and DNA with cofactor...
+Supramolecule #2: TnsC(1-503)
+Supramolecule #3: TnsD(1-318)
+Supramolecule #4: DNA
+Macromolecule #1: Transposon Tn7 transposition protein TnsC
+Macromolecule #2: Transposon Tn7 transposition protein TnsD
+Macromolecule #3: DNA (50-MER)
+Macromolecule #4: DNA (50-MER)
+Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #6: MAGNESIUM ION
+Macromolecule #7: ZINC ION
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 Details: 20 mM Tris pH 8.0, 150 mM NaCl, 1.4 mM beta-mercaptoethanol, 5 mM MgCl2 |
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 79.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: TnsC and TnsD were modelled using PDB 8GLU. |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-8glx: |