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Yorodumi- EMDB-19283: Conformational Landscape of the Type V-K CRISPR-associated Transp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19283 | |||||||||
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Title | Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K TnsC domain local-refinement map | |||||||||
Map data | CAST V-K TnsC domain local-refinement map | |||||||||
Sample |
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Keywords | CRISPR-associated Transposon genome editing transposition / DNA BINDING PROTEIN | |||||||||
Function / homology | Bacterial TniB / Bacterial TniB protein / : / P-loop containing nucleoside triphosphate hydrolase / TnsC Function and homology information | |||||||||
Biological species | Scytonema hofmannii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Tenjo-Castano F / Mesa P / Montoya G | |||||||||
Funding support | Denmark, European Union, 2 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Conformational landscape of the type V-K CRISPR-associated transposon integration assembly. Authors: Francisco Tenjo-Castaño / Nicholas Sofos / Luisa S Stutzke / Piero Temperini / Anders Fuglsang / Tillmann Pape / Pablo Mesa / Guillermo Montoya / Abstract: CRISPR-associated transposons (CASTs) are mobile genetic elements that co-opt CRISPR-Cas systems for RNA-guided DNA transposition. CASTs integrate large DNA cargos into the attachment (att) site ...CRISPR-associated transposons (CASTs) are mobile genetic elements that co-opt CRISPR-Cas systems for RNA-guided DNA transposition. CASTs integrate large DNA cargos into the attachment (att) site independently of homology-directed repair and thus hold promise for eukaryotic genome engineering. However, the functional diversity and complexity of CASTs hinder an understanding of their mechanisms. Here, we present the high-resolution cryoelectron microscopy (cryo-EM) structure of the reconstituted ∼1 MDa post-transposition complex of the type V-K CAST, together with different assembly intermediates and diverse TnsC filament lengths, thus enabling the recapitulation of the integration complex formation. The results of mutagenesis experiments probing the roles of specific residues and TnsB-binding sites show that transposition activity can be enhanced and suggest that the distance between the PAM and att sites is determined by the lengths of the TnsB C terminus and the TnsC filament. This singular model of RNA-guided transposition provides a foundation for repurposing the system for genome-editing applications. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19283.map.gz | 98.4 MB | EMDB map data format | |
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Header (meta data) | emd-19283-v30.xml emd-19283.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19283_fsc.xml | 28.5 KB | Display | FSC data file |
Images | emd_19283.png | 251.9 KB | ||
Masks | emd_19283_msk_1.map | 106.1 MB | Mask map | |
Filedesc metadata | emd-19283.cif.gz | 6.5 KB | ||
Others | emd_19283_half_map_1.map.gz emd_19283_half_map_2.map.gz | 98.6 MB 98.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19283 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19283 | HTTPS FTP |
-Validation report
Summary document | emd_19283_validation.pdf.gz | 1005.6 KB | Display | EMDB validaton report |
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Full document | emd_19283_full_validation.pdf.gz | 1005.2 KB | Display | |
Data in XML | emd_19283_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_19283_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19283 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19283 | HTTPS FTP |
-Related structure data
Related structure data | 8rkuMC 8axaC 8rduC 8rktC 8rkvC 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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-Map
File | Download / File: emd_19283.map.gz / Format: CCP4 / Size: 106.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CAST V-K TnsC domain local-refinement map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.728 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19283_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: CAST V-K TnsC domain local refinement, half-A map
File | emd_19283_half_map_1.map | ||||||||||||
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Annotation | CAST V-K TnsC domain local refinement, half-A map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CAST V-K TnsC domain local refinement, half-B map
File | emd_19283_half_map_2.map | ||||||||||||
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Annotation | CAST V-K TnsC domain local refinement, half-B map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type V-K CRISPR-associated transposon post-transposition state af...
Entire | Name: Type V-K CRISPR-associated transposon post-transposition state after transesterification |
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Components |
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-Supramolecule #1: Type V-K CRISPR-associated transposon post-transposition state af...
Supramolecule | Name: Type V-K CRISPR-associated transposon post-transposition state after transesterification type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
Molecular weight | Theoretical: 1 MDa |
-Macromolecule #1: Non-target strand - LE
Macromolecule | Name: Non-target strand - LE / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
Molecular weight | Theoretical: 20.961504 KDa |
Sequence | String: (DG)(DT)(DG)(DA)(DA)(DG)(DG)(DT)(DT)(DC) (DT)(DC)(DT)(DT)(DC)(DA)(DG)(DT)(DA)(DT) (DT)(DA)(DA)(DT)(DA)(DA)(DG)(DG)(DC) (DC)(DA)(DC)(DT)(DG)(DT)(DT)(DA)(DA)(DA) (DA) (DC)(DG)(DT)(DA)(DC)(DT) ...String: (DG)(DT)(DG)(DA)(DA)(DG)(DG)(DT)(DT)(DC) (DT)(DC)(DT)(DT)(DC)(DA)(DG)(DT)(DA)(DT) (DT)(DA)(DA)(DT)(DA)(DA)(DG)(DG)(DC) (DC)(DA)(DC)(DT)(DG)(DT)(DT)(DA)(DA)(DA) (DA) (DC)(DG)(DT)(DA)(DC)(DT)(DA)(DT) (DA)(DT)(DA)(DG)(DA)(DC)(DA)(DT)(DC)(DT) (DC)(DC) (DA)(DC)(DA)(DA)(DA)(DA)(DG) (DG) |
-Macromolecule #2: Target strand - LE
Macromolecule | Name: Target strand - LE / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
Molecular weight | Theoretical: 40.82216 KDa |
Sequence | String: (DA)(DA)(DT)(DT)(DA)(DA)(DA)(DT)(DA)(DG) (DT)(DC)(DA)(DC)(DA)(DA)(DT)(DG)(DA)(DC) (DA)(DT)(DT)(DA)(DA)(DT)(DC)(DT)(DG) (DT)(DC)(DA)(DC)(DC)(DG)(DA)(DC)(DG)(DA) (DC) (DA)(DG)(DA)(DT)(DA)(DA) ...String: (DA)(DA)(DT)(DT)(DA)(DA)(DA)(DT)(DA)(DG) (DT)(DC)(DA)(DC)(DA)(DA)(DT)(DG)(DA)(DC) (DA)(DT)(DT)(DA)(DA)(DT)(DC)(DT)(DG) (DT)(DC)(DA)(DC)(DC)(DG)(DA)(DC)(DG)(DA) (DC) (DA)(DG)(DA)(DT)(DA)(DA)(DT)(DT) (DT)(DG)(DT)(DC)(DA)(DC)(DT)(DG)(DT)(DA) (DC)(DA) (DC)(DT)(DA)(DC)(DG)(DC)(DC) (DT)(DT)(DT)(DT)(DG)(DT)(DG)(DG)(DA)(DG) (DA)(DT)(DG) (DT)(DC)(DT)(DA)(DA)(DT) (DA)(DT)(DC)(DT)(DA)(DC)(DG)(DT)(DT)(DT) (DT)(DA)(DA)(DC) (DA)(DG)(DT)(DG)(DG) (DC)(DC)(DT)(DT)(DA)(DT)(DT)(DA)(DA)(DA) (DT)(DG)(DA)(DC)(DT) (DT)(DC)(DT)(DC) (DA)(DA)(DC)(DC)(DT)(DT)(DC)(DA)(DC) |
-Macromolecule #3: ShTnsC
Macromolecule | Name: ShTnsC / type: protein_or_peptide / ID: 3 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: Scytonema hofmannii (bacteria) |
Molecular weight | Theoretical: 31.400496 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: STEAQAIAKQ LGGVKPDDEW LQAEIARLKG KSIVPLQQVK TLHDWLDGKR KARKSCRVVG ESRTGKTVAC DAYRYRHKPQ QEAGRPPTV PVVYIRPHQK CGPKDLFKKI TEYLKYRVTK GTVSDFRDRT IEVLKGCGVE MLIIDEADRL KPETFADVRD I AEDLGIAV ...String: STEAQAIAKQ LGGVKPDDEW LQAEIARLKG KSIVPLQQVK TLHDWLDGKR KARKSCRVVG ESRTGKTVAC DAYRYRHKPQ QEAGRPPTV PVVYIRPHQK CGPKDLFKKI TEYLKYRVTK GTVSDFRDRT IEVLKGCGVE MLIIDEADRL KPETFADVRD I AEDLGIAV VLVGTDRLDA VIKRDEQVLE RFRAHLRFGK LSGEDFKNTV EMWEQMVLKL PVSSNLKSKE MLRILTSATE GY IGRLDEI LREAAIRSLS RGLKKIDKAV LQEVAKEYK UniProtKB: TnsC |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 14 / 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: 14 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 538 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: UltrAuFoil R0./1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 19936 / Average electron dose: 40.0 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: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Protocol: AB INITIO MODEL |
Output model | PDB-8rku: |