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Yorodumi- EMDB-43616: Structure of HamB-DNA complex, conformation 2, from the Escherich... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43616 | |||||||||
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Title | Structure of HamB-DNA complex, conformation 2, from the Escherichia coli Hachiman defense system | |||||||||
Map data | Sharp map of conformation 2 of the HamB-DNA complex | |||||||||
Sample |
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Keywords | Helicase-DNA complex / antiphage defense system / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex | |||||||||
Function / homology | Function and homology information helicase activity / nucleic acid binding / hydrolase activity / ATP binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.93 Å | |||||||||
Authors | Tuck OT / Doudna JA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: bioRxiv / Year: 2024 Title: Hachiman is a genome integrity sensor. Authors: Owen T Tuck / Benjamin A Adler / Emily G Armbruster / Arushi Lahiri / Jason J Hu / Julia Zhou / Joe Pogliano / Jennifer A Doudna / Abstract: Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman comprises a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown ...Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman comprises a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact dsDNA. When the HamAB complex detects DNA damage, HamB helicase activity liberates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating 'phantom' cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and eukaryotic enzymes suggest this bacterial immune system has been repurposed for diverse functions across all domains of life. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43616.map.gz | 57 MB | EMDB map data format | |
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Header (meta data) | emd-43616-v30.xml emd-43616.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43616_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_43616.png | 76.2 KB | ||
Masks | emd_43616_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-43616.cif.gz | 7.2 KB | ||
Others | emd_43616_additional_1.map.gz emd_43616_half_map_1.map.gz emd_43616_half_map_2.map.gz | 32.3 MB 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43616 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43616 | HTTPS FTP |
-Validation report
Summary document | emd_43616_validation.pdf.gz | 702.7 KB | Display | EMDB validaton report |
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Full document | emd_43616_full_validation.pdf.gz | 702.3 KB | Display | |
Data in XML | emd_43616_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_43616_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43616 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43616 | HTTPS FTP |
-Related structure data
Related structure data | 8vxcMC 8vx9C 8vxaC 8vxyC 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_43616.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharp map of conformation 2 of the HamB-DNA complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.115 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43616_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map of conformation 2 of the HamB-DNA complex
File | emd_43616_additional_1.map | ||||||||||||
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Annotation | Unsharpened map of conformation 2 of the HamB-DNA complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of conformation 2 of the HamB-DNA complex
File | emd_43616_half_map_1.map | ||||||||||||
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Annotation | Half map A of conformation 2 of the HamB-DNA complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of conformation 2 of the HamB-DNA complex
File | emd_43616_half_map_2.map | ||||||||||||
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Annotation | Half map B of conformation 2 of the HamB-DNA complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HamB-DNA complex
Entire | Name: HamB-DNA complex |
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Components |
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-Supramolecule #1: HamB-DNA complex
Supramolecule | Name: HamB-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: ECOR31 |
Molecular weight | Theoretical: 155 KDa |
-Macromolecule #1: DNA (40-MER)
Macromolecule | Name: DNA (40-MER) / type: dna / ID: 1 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 12.154847 KDa |
Sequence | String: (DT)(DC)(DG)(DT)(DC)(DA)(DC)(DC)(DA)(DG) (DT)(DA)(DC)(DA)(DA)(DA)(DC)(DT)(DA)(DC) (DA)(DA)(DC)(DG)(DC)(DC)(DT)(DG)(DT) (DA)(DG)(DC)(DA)(DT)(DT)(DC)(DC)(DA)(DC) (DA) |
-Macromolecule #2: HamB
Macromolecule | Name: HamB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: ECOR31 |
Molecular weight | Theoretical: 130.898453 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPATADEIIE AIKEASAVGF RGRLIARGQA RSVIWRDGDL PPDAPEFSAL LSQDLQGYAY ALIDLGLRLR ELNGDDAYAR IAFEQAGTA LESAIAKGKR DSRDTDFHFV MAAASYHLAH LSARAYSLLA MVGQDDNFSP IERALTQLIR RDLRTLRDNA L GFRLRGDG ...String: MPATADEIIE AIKEASAVGF RGRLIARGQA RSVIWRDGDL PPDAPEFSAL LSQDLQGYAY ALIDLGLRLR ELNGDDAYAR IAFEQAGTA LESAIAKGKR DSRDTDFHFV MAAASYHLAH LSARAYSLLA MVGQDDNFSP IERALTQLIR RDLRTLRDNA L GFRLRGDG SDVKITEILQ ARLNLPQDEN GDSESEEDIL FDGLDLALTD AYMSAISLYL LAVERGESRL LSRAIEKLRI SL SICAQFN MLPQWWLNFI TIHLLSDLWS DTFHERLPLV PVGGDAAEWP ALRELFIALL QRRPRAEIDL WPSQREAAGR SVN DNDDLV VSLPTSAGKT RIAELCILRC LAGGKRVVFI TPLRALSAQT EATLSRTFGP LGKTISMLYG SIGVSGMDED AIRQ RDIVV ATPEKLDFAL RNDPSIINDV GLFIFDEGHM IGADEREVRY EVQIQRLLRR QDADTRRIVC LSAILPDGEQ LDDFA GWLR RDKPGGPIKN NWRPTRLQFG EVIWSAPAGR LNLSVGYEAA WVSRFIVSRQ PPKVKLPNKK QRTKMFPSDN KELCLA TAW RLIEDGQTVL IYCPLRRSVE PFAETIVDLH QRGLLPSLFD AAPDILDTAI SLGEEWLGAH SPILACLRLG VALHHGA LP TAYRKEIERL LRDGVLKVTI SSPTLAQGLN LSATAIVMHS LHRNRELIKV SEFRNVIGRA GRAYVDVEGL VIYPIFDK V NKRQTNWHTL TSDTGAREME SGLIQLVCVL LIRMHTRLGG DLKALTEYVT NNAVAWEFPE IMTESPQERD IAQAIWEKQ LSTLDTAILS LLGENDIPDD QIETALDDIL QSSLWQRSLQ RYRDENERIL LKSGLLSRSR YIWQRSTAAG RRGYFLSGVG LTTGLRLDA IAAKANQLLI DANAAIMGGD AEEAIAAITA LAEEVFTFYP FIPDPLPGDW RGILRSWLLG EPMTNVANTQ A SETLQFVE NGLVYRLPWA MEAIRVRATA NGDLIGDTDT TLDDYELGFA VAAVETGTLS RSSSLLIQAG FSSRLAAIKV VT DTTADFQ SGQELRRWLN SEEVISHTDN HDWPTPETRV MWLEFLGSLS PKGSQVWSRH RYNGMVDWRD TPAVIGTPLQ LYT VDGIHH VLADDGTPLG SINGRINTNR RGLLRVEVDD ENGRAMFDYL GPDDFIST UniProtKB: DEAD/DEAH box helicase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9133 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: v1.4.0 |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-8vxc: |