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Yorodumi- EMDB-13909: Cryo-EM structure of Tn4430 TnpA transposase from Tn3 family in c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13909 | |||||||||||||||
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Title | Cryo-EM structure of Tn4430 TnpA transposase from Tn3 family in complex with strand-transfer like DNA product | |||||||||||||||
Map data | map local filtered in RELION3.1 used for refinement | |||||||||||||||
Sample |
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Keywords | DNA transposition / Tn3 family / antibiotic resistance / protein metamorphosis / RECOMBINATION | |||||||||||||||
Function / homology | Tn3 transposase DDE domain / Domain of unknown function DUF4158 / : / Tn3 transposase DDE domain / Domain of unknown function (DUF4158) / transposase activity / DNA transposition / DNA binding / Transposase for transposon Tn4430 Function and homology information | |||||||||||||||
Biological species | Bacillus thuringiensis (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | Shkumatov AV / Oger CA / Aryanpour N / Hallet BF / Efremov RG | |||||||||||||||
Funding support | Belgium, 4 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural insight into Tn3 family transposition mechanism. Authors: Alexander V Shkumatov / Nicolas Aryanpour / Cédric A Oger / Gérôme Goossens / Bernard F Hallet / Rouslan G Efremov / Abstract: Transposons are diverse mobile genetic elements that play the critical role as genome architects in all domains of life. Tn3 is a widespread family and among the first identified bacterial ...Transposons are diverse mobile genetic elements that play the critical role as genome architects in all domains of life. Tn3 is a widespread family and among the first identified bacterial transposons famed for their contribution to the dissemination of antibiotic resistance. Transposition within this family is mediated by a large TnpA transposase, which facilitates both transposition and target immunity. Howtever, a structural framework required for understanding the mechanism of TnpA transposition is lacking. Here, we describe the cryo-EM structures of TnpA from Tn4430 in the apo form and paired with transposon ends before and after DNA cleavage and strand transfer. We show that TnpA has an unusual architecture and exhibits a family specific regulatory mechanism involving metamorphic refolding of the RNase H-like catalytic domain. The TnpA structure, constrained by a double dimerization interface, creates a peculiar topology that suggests a specific role for the target DNA in transpososome assembly and activation. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13909.map.gz | 191.1 MB | EMDB map data format | |
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Header (meta data) | emd-13909-v30.xml emd-13909.xml | 22.9 KB 22.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13909_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_13909.png | 99.7 KB | ||
Masks | emd_13909_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-13909.cif.gz | 7.2 KB | ||
Others | emd_13909_half_map_1.map.gz emd_13909_half_map_2.map.gz | 259.6 MB 259.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13909 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13909 | HTTPS FTP |
-Validation report
Summary document | emd_13909_validation.pdf.gz | 837.3 KB | Display | EMDB validaton report |
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Full document | emd_13909_full_validation.pdf.gz | 836.8 KB | Display | |
Data in XML | emd_13909_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | emd_13909_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13909 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13909 | HTTPS FTP |
-Related structure data
Related structure data | 7qd6MC 7qd4C 7qd5C 7qd8C 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_13909.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | map local filtered in RELION3.1 used for refinement | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.76 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13909_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_13909_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_13909_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TnpA-IR71st complex
Entire | Name: TnpA-IR71st complex |
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Components |
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-Supramolecule #1: TnpA-IR71st complex
Supramolecule | Name: TnpA-IR71st complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: hyperactive TnpA mutant S911R in complex with 71 bp branched DNA substrate containing trasnposon recognition sequence. |
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-Supramolecule #2: hyperactive TnpA mutant S911R
Supramolecule | Name: hyperactive TnpA mutant S911R / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: hyperactive TnpA mutant S911R |
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Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
-Supramolecule #3: DNA substrate
Supramolecule | Name: DNA substrate / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: DNA substrate |
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Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
-Macromolecule #1: Transposase for transposon Tn4430
Macromolecule | Name: Transposase for transposon Tn4430 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
Molecular weight | Theoretical: 116.992117 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGVKQLLSEA QRNELMDLSR LTEWDLVTFH TFSKHDLHLI LKHRRGYNRL GFALQLVLIR YPGWSLTEYK DIPQYVVAYV ASQLQIPPE EFLVYAKRGN TLWEHLGEIR TEYGYQNFSS EYKETLLQFL VQQAMDNNNT LYLIEITIST LRKMKVILPA M YVIEDIVW ...String: MGVKQLLSEA QRNELMDLSR LTEWDLVTFH TFSKHDLHLI LKHRRGYNRL GFALQLVLIR YPGWSLTEYK DIPQYVVAYV ASQLQIPPE EFLVYAKRGN TLWEHLGEIR TEYGYQNFSS EYKETLLQFL VQQAMDNNNT LYLIEITIST LRKMKVILPA M YVIEDIVW EAKQQADQKV YSILHDGLVQ EQKDQLDALL LPTINGKSPL AWLKDVPAQP SPESFLKVID RLQFVQKIGL TI DTTKINT NRLRQLARLG SKYEPYAFRR FNEVKRYSML VSFLLEITQD LIDYAIEIHD RLMMNLQTKG KKEQDEIQQA NGK KLNEKI LQFITVCGTL IEAKETGKDA FAALDEVMSW NEMVESVEEA KQLSRPLNYD YLDLLNTRYS YVRRYAPTLL RSLH FRATK SGEPVLQALD TIHELNETGK RKVPHGAPLH FVSNRWQKHV YDDDGNINRH YYELAALTEL RNHIRSGDIF VSGSR HHKA FDDYLIPYDE WNEVSNIPNG LTAPLKAEDY ITDRINRLNE HLEWLSKNSE KLEGVDISQG KLHVERLDRG TPEEAK AFS KLLHSMLPRI KLTDLLIEVA SWTGFHDQFI HASTNQSPDQ EEQNIVLATL MAMGTNIGLT KMAEATPGIS YRQMANA SQ WRMYDDAMVR AQSILVNFQK EQKLSSYWGD GTTSSSDGMR LSIAVRSLHA DSNPHYGTGK GGTIYRFVSD QLSAYHVK V ITTNARDALH VLDGLLHHET DLKIEEHYTD TAGYTDQVFA LTHLLGFRFA PRIRDLADTK LFSIPGGEEY ENVQALLKG KINVKLIKEN YEDIRRLAYS VQTGKVSSAL IMGKLGSYAR QNKLATALGE MGRIEKTLFT LDYISNKAVR RRVQKGLNKG EAINALARI IFFGQRGEFR ERALQDQLQR ARALNIIINA ISVWNTVYME KAVEELKARG EFREDLMPYA WPLGWEHINF L GEYKFEGL HDTGQMNLRP LRIKEPFYSP IRSFLEQKLI SEEDLNSAVD HHHHHH UniProtKB: Transposase for transposon Tn4430 |
-Macromolecule #2: IR71st non transferred strand
Macromolecule | Name: IR71st non transferred strand / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
Molecular weight | Theoretical: 21.85801 KDa |
Sequence | String: (DC)(DT)(DC)(DT)(DA)(DG)(DC)(DT)(DC)(DG) (DA)(DG)(DA)(DT)(DG)(DC)(DA)(DT)(DC)(DC) (DA)(DT)(DG)(DG)(DG)(DG)(DG)(DT)(DA) (DC)(DC)(DG)(DC)(DC)(DA)(DG)(DC)(DA)(DT) (DT) (DT)(DC)(DG)(DG)(DA)(DA) ...String: (DC)(DT)(DC)(DT)(DA)(DG)(DC)(DT)(DC)(DG) (DA)(DG)(DA)(DT)(DG)(DC)(DA)(DT)(DC)(DC) (DA)(DT)(DG)(DG)(DG)(DG)(DG)(DT)(DA) (DC)(DC)(DG)(DC)(DC)(DA)(DG)(DC)(DA)(DT) (DT) (DT)(DC)(DG)(DG)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DC)(DC)(DA)(DC)(DG)(DC)(DT) (DA)(DA) (DG)(DA)(DT)(DC)(DC)(DT)(DC) (DT)(DA)(DG)(DG) |
-Macromolecule #3: IR71st transferred strand
Macromolecule | Name: IR71st transferred strand / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
Molecular weight | Theoretical: 24.127393 KDa |
Sequence | String: (DG)(DG)(DC)(DA)(DA)(DA)(DG)(DA)(DT)(DG) (DT)(DC)(DC)(DT)(DA)(DG)(DT)(DT)(DT)(DA) (DG)(DT)(DT)(DG)(DG)(DC)(DT)(DG)(DA) (DT)(DC)(DC)(DT)(DA)(DG)(DA)(DG)(DG)(DA) (DT) (DC)(DT)(DT)(DA)(DG)(DC) ...String: (DG)(DG)(DC)(DA)(DA)(DA)(DG)(DA)(DT)(DG) (DT)(DC)(DC)(DT)(DA)(DG)(DT)(DT)(DT)(DA) (DG)(DT)(DT)(DG)(DG)(DC)(DT)(DG)(DA) (DT)(DC)(DC)(DT)(DA)(DG)(DA)(DG)(DG)(DA) (DT) (DC)(DT)(DT)(DA)(DG)(DC)(DG)(DT) (DG)(DG)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC) (DC)(DG) (DA)(DA)(DA)(DT)(DG)(DC)(DT) (DG)(DG)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC) (DC) |
-Macromolecule #4: IR71st transferred strand
Macromolecule | Name: IR71st transferred strand / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
Molecular weight | Theoretical: 7.105598 KDa |
Sequence | String: (DC)(DA)(DT)(DG)(DG)(DA)(DT)(DG)(DC)(DA) (DT)(DC)(DT)(DC)(DG)(DA)(DG)(DC)(DT)(DA) (DG)(DA)(DG) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 7.5 / Details: 50 mM HEPES (pH 7.5), 100 mM NaCl, 30 mM L-Arg HCL |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 4155 / Average exposure time: 3.0 sec. / Average electron dose: 62.0 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: 3.2 µm / Nominal defocus min: 0.4 µm |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 167.8 / Target criteria: correlation coefficient |
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Output model | PDB-7qd6: |