+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28048 | |||||||||
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Title | Structure of focused PtuA(dimer) and PtuB(monomer) complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | PtuA / IMMUNE SYSTEM | |||||||||
Function / homology | Retron Ec78 putative HNH endonuclease-like / TIGR02646 family protein Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.72 Å | |||||||||
Authors | Shen ZF / Fu TM | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: PtuA and PtuB assemble into an inflammasome-like oligomer for anti-phage defense. Authors: Yuanyuan Li / Zhangfei Shen / Mengyuan Zhang / Xiao-Yuan Yang / Sean P Cleary / Jiale Xie / Ila A Marathe / Marius Kostelic / Jacelyn Greenwald / Anthony D Rish / Vicki H Wysocki / Chong ...Authors: Yuanyuan Li / Zhangfei Shen / Mengyuan Zhang / Xiao-Yuan Yang / Sean P Cleary / Jiale Xie / Ila A Marathe / Marius Kostelic / Jacelyn Greenwald / Anthony D Rish / Vicki H Wysocki / Chong Chen / Qiang Chen / Tian-Min Fu / Yamei Yu / Abstract: Escherichia coli Septu system, an anti-phage defense system, comprises two components: PtuA and PtuB. PtuA contains an ATPase domain, while PtuB is predicted to function as a nuclease. Here we show ...Escherichia coli Septu system, an anti-phage defense system, comprises two components: PtuA and PtuB. PtuA contains an ATPase domain, while PtuB is predicted to function as a nuclease. Here we show that PtuA and PtuB form a stable complex with a 6:2 stoichiometry. Cryo-electron microscopy structure of PtuAB reveals a distinctive horseshoe-like configuration. PtuA adopts a hexameric arrangement, organized as an asymmetric trimer of dimers, contrasting the ring-like structure by other ATPases. Notably, the three pairs of PtuA dimers assume distinct conformations and fulfill unique roles in recruiting PtuB. Our functional assays have further illuminated the importance of the oligomeric assembly of PtuAB in anti-phage defense. Moreover, we have uncovered that ATP molecules can directly bind to PtuA and inhibit the activities of PtuAB. Together, the assembly and function of the Septu system shed light on understanding other ATPase-containing systems in bacterial immunity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28048.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-28048-v30.xml emd-28048.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28048_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_28048.png | 41.6 KB | ||
Masks | emd_28048_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-28048.cif.gz | 5.7 KB | ||
Others | emd_28048_half_map_1.map.gz emd_28048_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28048 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28048 | HTTPS FTP |
-Validation report
Summary document | emd_28048_validation.pdf.gz | 896.7 KB | Display | EMDB validaton report |
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Full document | emd_28048_full_validation.pdf.gz | 896.3 KB | Display | |
Data in XML | emd_28048_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_28048_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28048 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28048 | HTTPS FTP |
-Related structure data
Related structure data | 8ee7MC 8ee4C 8eeaC 8suxC 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_28048.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28048_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28048_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28048_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 6 ptuA form as a complex
Entire | Name: 6 ptuA form as a complex |
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Components |
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-Supramolecule #1: 6 ptuA form as a complex
Supramolecule | Name: 6 ptuA form as a complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: PtuA
Macromolecule | Name: PtuA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 53.189656 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MRIDKLSLLN FRCFKQLDIT FDEHITILVA PNGAGKTTVL DAVRLALFPF IRGFDASLYV KDKSLAIRTE DLRLIYRQEA LNMEMSSPA KITATGEWAS GKTATWMLDK RGEQPPHEDK MAAQLTRWGE QLQKRVREEH SLQQVELPLM LYLGTARLWY Q ERYEKQPT ...String: MRIDKLSLLN FRCFKQLDIT FDEHITILVA PNGAGKTTVL DAVRLALFPF IRGFDASLYV KDKSLAIRTE DLRLIYRQEA LNMEMSSPA KITATGEWAS GKTATWMLDK RGEQPPHEDK MAAQLTRWGE QLQKRVREEH SLQQVELPLM LYLGTARLWY Q ERYEKQPT EQRLDNSAFS RLSGYDDCLS ATSNYKQFEQ WYSWLWLSYR EHQITQLESP SAKLKEGVRV QRMKEAIQAI QQ AINCLTQ QVTGWHDLEY SASHNQQLVM SHPQYGKIPL SQLSDGLRNA VAMVADIAFR CVKLNPHLQN DAALKTQGIV LID EVDMFL HPAWQQQIIQ SLRSAFPQIQ FIVTTHSPQV LSTVKRESIR LLEQDENGNG KALMPLGATY GEPSNDVLQS VMGV DPQPA VKEKADLQKL TGWVDQGKYD EPKTQQLMVA LEVALGEKHP QLQRLQRSIA RQRLLKGKAQ |
-Macromolecule #2: PtuB
Macromolecule | Name: PtuB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 28.136291 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MRHVIKTQLG TVALLTAHEN PPQDADQSTR RWRNFRRDKA AVMVQLINEQ YHLCCYSEIR SDLRGLGYHI EHVENKSQHP ERTFDYQNL AASALDSGEN GGLSSLKGKN AFGGHAQGKQ DVVDMAKFIH CHIRDCSRYF AYLSDGRIVP ADELNAQETE N AQYTIDLL ...String: MRHVIKTQLG TVALLTAHEN PPQDADQSTR RWRNFRRDKA AVMVQLINEQ YHLCCYSEIR SDLRGLGYHI EHVENKSQHP ERTFDYQNL AASALDSGEN GGLSSLKGKN AFGGHAQGKQ DVVDMAKFIH CHIRDCSRYF AYLSDGRIVP ADELNAQETE N AQYTIDLL NLNSGFLQTE RRNHWEELEQ LFDEHIEKDW DLQQLLQLDL VSTPDHKLHE FFSITRQFFQ QEAEQVLQSH AP ALI UniProtKB: TIGR02646 family protein |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / 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 | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |