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- EMDB-43643: Structure of HamA(E138A,K140A)B-plasmid DNA complex from the Esch... -
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Open data
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Basic information
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Title | Structure of HamA(E138A,K140A)B-plasmid DNA complex from the Escherichia coli Hachiman defense system | |||||||||
![]() | Sharp map of nuclease-deficient HamAB-plasmid DNA complex | |||||||||
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![]() | Nuclease-helicase complex / antiphage defense system / ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Tuck OT / Hu JJ / Doudna JA | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 59.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.4 KB 25.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 68.5 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7.4 KB | ||
Others | ![]() ![]() ![]() | 32.2 MB 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vxyMC ![]() 8vx9C ![]() 8vxaC ![]() 8vxcC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Sharp map of nuclease-deficient HamAB-plasmid DNA complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 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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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map of nuclease-deficient HamAB-plasmid DNA complex
File | emd_43643_additional_1.map | ||||||||||||
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Annotation | Unsharpened map of nuclease-deficient HamAB-plasmid DNA complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of nuclease-deficient HamAB-plasmid DNA complex
File | emd_43643_half_map_1.map | ||||||||||||
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Annotation | Half map B of nuclease-deficient HamAB-plasmid DNA complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of nuclease-deficient HamAB-plasmid DNA complex
File | emd_43643_half_map_2.map | ||||||||||||
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Annotation | Half map A of nuclease-deficient HamAB-plasmid DNA complex | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : HamA(E138A,K140A)B-plasmid DNA complex
Entire | Name: HamA(E138A,K140A)B-plasmid DNA complex |
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Components |
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-Supramolecule #1: HamA(E138A,K140A)B-plasmid DNA complex
Supramolecule | Name: HamA(E138A,K140A)B-plasmid DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#4 |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Macromolecule #1: Plasmid DNA
Macromolecule | Name: Plasmid DNA / type: dna / ID: 1 / Details: unknown sequence / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 9.38502 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT) |
-Macromolecule #2: Plasmid DNA
Macromolecule | Name: Plasmid DNA / type: dna / ID: 2 / Details: unknown sequence / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 9.664453 KDa |
Sequence | String: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA) |
-Macromolecule #3: HamA
Macromolecule | Name: HamA / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 28.807664 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MANFEDWCDS TERNISDHYL QSITARDAEC MFGVQVMAAL IPEHYASPRN IANAFEALGK PGLAAYIAGK LPETKQIRSG DLGEIFATE WINARSNGYK TPIKRLRWKD HRNMSMRGED VIGIYIDQSS QQLFFLKTAA ASRAKMTGEV VSEARDNLNK E QGLPSSHA ...String: MANFEDWCDS TERNISDHYL QSITARDAEC MFGVQVMAAL IPEHYASPRN IANAFEALGK PGLAAYIAGK LPETKQIRSG DLGEIFATE WINARSNGYK TPIKRLRWKD HRNMSMRGED VIGIYIDQSS QQLFFLKTAA ASRAKMTGEV VSEARDNLNK E QGLPSSHA LMFIADRLNE QGEELLAKAI LNATLRQGIV PGCVRHLIFL LSGNSSETML TTSIEKYTGQ NNQWGVCLRI AR HGEFIAA TFEKVISDAS NS UniProtKB: DUF1837 domain-containing protein |
-Macromolecule #4: HamB
Macromolecule | Name: HamB / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 130.898453 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil 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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3724 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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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-8vxy: |