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Yorodumi- EMDB-38205: Cryo-EM structure of an anti-phage defense complex bound to AMPPN... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38205 | |||||||||
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Title | Cryo-EM structure of an anti-phage defense complex bound to AMPPNP and DNA at state 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | HerA / Helicase DUF4297 / Endonuclease / DNA BINDING PROTEIN | |||||||||
Function / homology | : / : Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.73 Å | |||||||||
Authors | An Q / Deng Z | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Res / Year: 2024 Title: Molecular and structural basis of an ATPase-nuclease dual-enzyme anti-phage defense complex. Authors: Qiyin An / Yong Wang / Zhenhua Tian / Jie Han / Jinyue Li / Fumeng Liao / Feiyang Yu / Haiyan Zhao / Yancheng Wen / Heng Zhang / Zengqin Deng / Abstract: Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in ...Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in the type III CRISPR-Cas system. However, concerted enzymatic activities in other bacterial defense systems are poorly understood. Here, we biochemically and structurally characterize a two-component defense system DUF4297-HerA, demonstrating that DUF4297-HerA confers resistance against phage infection by cooperatively cleaving dsDNA and hydrolyzing ATP. DUF4297 alone forms a dimer, and HerA alone exists as a nonplanar split spiral hexamer, both of which exhibit extremely low enzymatic activity. Interestingly, DUF4297 and HerA assemble into an approximately 1 MDa supramolecular complex, where two layers of DUF4297 (6 DUF4297 molecules per layer) linked via inter-layer dimerization of neighboring DUF4297 molecules are stacked on top of the HerA hexamer. Importantly, the complex assembly promotes dimerization of DUF4297 molecules in the upper layer and enables a transition of HerA from a nonplanar hexamer to a planar hexamer, thus activating their respective enzymatic activities to abrogate phage infection. Together, our findings not only characterize a novel dual-enzyme anti-phage defense system, but also reveal a unique activation mechanism by cooperative complex assembly in bacterial immunity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38205.map.gz | 118.1 MB | EMDB map data format | |
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Header (meta data) | emd-38205-v30.xml emd-38205.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38205_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_38205.png | 29.9 KB | ||
Filedesc metadata | emd-38205.cif.gz | 6.2 KB | ||
Others | emd_38205_half_map_1.map.gz emd_38205_half_map_2.map.gz | 116.2 MB 116.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38205 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38205 | HTTPS FTP |
-Validation report
Summary document | emd_38205_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_38205_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_38205_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_38205_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38205 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38205 | HTTPS FTP |
-Related structure data
Related structure data | 8xawMC 8xauC 8xavC 8xaxC 8xayC M: atomic model generated by this map C: citing same article (ref.) |
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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_38205.map.gz / Format: CCP4 / Size: 125 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: 0.95 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38205_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38205_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DUF4297-HerA-DNA-state2
Entire | Name: DUF4297-HerA-DNA-state2 |
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Components |
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-Supramolecule #1: DUF4297-HerA-DNA-state2
Supramolecule | Name: DUF4297-HerA-DNA-state2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: ATP-binding protein
Macromolecule | Name: ATP-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 64.870047 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSRNNDINAE VVSVSPNKLK ISVDDLEEFK IAEEKLGVGS YLRVSDNQDV ALLAIIDNFS IEVKESQKQK YMIEASPIGL VKNGKFYRG GDSLALPPKK VEPAKLDEII SIYSDSIDIN DRFTFSSLSL NTKVSVPVNG NRFFNKHIAI VGSTGSGKSH T VAKILQKA ...String: MSRNNDINAE VVSVSPNKLK ISVDDLEEFK IAEEKLGVGS YLRVSDNQDV ALLAIIDNFS IEVKESQKQK YMIEASPIGL VKNGKFYRG GDSLALPPKK VEPAKLDEII SIYSDSIDIN DRFTFSSLSL NTKVSVPVNG NRFFNKHIAI VGSTGSGKSH T VAKILQKA VDEKQEGYKG LNNSHIIIFD IHSEYENAFP NSNVLNVDTL TLPYWLLNGD ELEELFLDTE ANDHNQRNVF RQ AITLNKK IHFQGDPATK EIISFHSPYY FDINEVINYI NNRNNERKNK DNEHIWSDEE GNFKFDNENA HRLFKENVTP DGS SAGALN GKLLNFVDRL QSKIFDKRLD FILGEGSKSV TFKETLETLI SYGKDKSNIT ILDVSGVPFE VLSICVSLIS RLIF EFGYH SKKIKRKSNE NQDIPILIVY EEAHKYAPKS DLSKYRTSKE AIERIAKEGR KYGVTLLLAS QRPSEISETI FSQCN TFIS MRLTNPDDQN YVKRLLPDTV GDITNLLPSL KEGEALIMGD SISIPSIVKI EKCTIPPSSI DIKYLDEWRK EWVDSE FDK IIEQWSKS UniProtKB: UNIPROTKB: A0A9X9SUP5 |
-Macromolecule #2: DUF4297
Macromolecule | Name: DUF4297 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 46.971949 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDRSAVDTIR GYCYQVDKTI IEIFSLPQMD DSIDIECIED VDVYNDGHLT AIQCKYYEST DYNHSVISKP IRLMLSHFKD NKEKGANYY LYGHYKSGQE KLTLPLKVDF FKSNFLTYTE KKIKHEYHIE NGLTEEDLQA FLDRLVININ AKSFDDQKKE T IQIIKNHF ...String: MDRSAVDTIR GYCYQVDKTI IEIFSLPQMD DSIDIECIED VDVYNDGHLT AIQCKYYEST DYNHSVISKP IRLMLSHFKD NKEKGANYY LYGHYKSGQE KLTLPLKVDF FKSNFLTYTE KKIKHEYHIE NGLTEEDLQA FLDRLVININ AKSFDDQKKE T IQIIKNHF QCEDYEAEHY LYSNAFRKTY DISCNKKDRR IKKSDFVESI NKSKVLFNIW FYQYEGRKEY LRKLKESFIR RS VNTSPYA RFFILEFQDK TDIKTVKDCI YKIQSNWSNL SKRTDRPYSP FLLFHGTSDA NLYELKNQLF NEDLIFTDGY PFK GSVFTP KMLIEGFSNK EIHFQFINDI DDFNETLNSI NIRKEVYQFY TENCLDIPSQ LPQVNIQVKD FADIKEIV UniProtKB: UNIPROTKB: A0A9X9SUN3 |
-Macromolecule #3: S20DNA1
Macromolecule | Name: S20DNA1 / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 18.035535 KDa |
Sequence | String: (DG)(DA)(DT)(DC)(DC)(DA)(DT)(DG)(DC)(DG) (DC)(DG)(DT)(DT)(DG)(DA)(DC)(DA)(DG)(DT) (DC)(DA)(DC)(DC)(DT)(DC)(DT)(DT)(DA) (DC)(DA)(DT)(DT)(DC)(DC)(DT)(DC)(DA)(DA) (DC) (DT)(DG)(DG)(DA)(DC)(DT) ...String: (DG)(DA)(DT)(DC)(DC)(DA)(DT)(DG)(DC)(DG) (DC)(DG)(DT)(DT)(DG)(DA)(DC)(DA)(DG)(DT) (DC)(DA)(DC)(DC)(DT)(DC)(DT)(DT)(DA) (DC)(DA)(DT)(DT)(DC)(DC)(DT)(DC)(DA)(DA) (DC) (DT)(DG)(DG)(DA)(DC)(DT)(DG)(DA) (DC)(DG)(DG)(DA)(DT)(DC)(DC)(DG)(DC)(DC) (DG) |
-Macromolecule #4: S20DNA2
Macromolecule | Name: S20DNA2 / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 18.333727 KDa |
Sequence | String: (DC)(DG)(DG)(DC)(DG)(DG)(DA)(DT)(DC)(DC) (DG)(DT)(DC)(DA)(DG)(DT)(DC)(DC)(DA)(DG) (DT)(DT)(DG)(DA)(DG)(DG)(DA)(DA)(DT) (DG)(DT)(DA)(DA)(DG)(DA)(DG)(DG)(DT)(DG) (DA) (DC)(DT)(DG)(DT)(DC)(DA) ...String: (DC)(DG)(DG)(DC)(DG)(DG)(DA)(DT)(DC)(DC) (DG)(DT)(DC)(DA)(DG)(DT)(DC)(DC)(DA)(DG) (DT)(DT)(DG)(DA)(DG)(DG)(DA)(DA)(DT) (DG)(DT)(DA)(DA)(DG)(DA)(DG)(DG)(DT)(DG) (DA) (DC)(DT)(DG)(DT)(DC)(DA)(DA)(DC) (DG)(DC)(DG)(DC)(DA)(DT)(DG)(DG)(DA)(DT) (DC) |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 3 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 3 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / 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: 2.5 µm / Nominal defocus min: 0.5 µm |