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Open data
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Basic information
Entry | Database: PDB / ID: 8ee7 | ||||||
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Title | Structure of focused PtuA(dimer) and PtuB(monomer) complex | ||||||
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![]() | IMMUNE SYSTEM / PtuA | ||||||
Function / homology | Retron Ec78 putative HNH endonuclease-like / ADENOSINE-5'-TRIPHOSPHATE / TIGR02646 family protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å | ||||||
![]() | Shen, Z.F. / Fu, T.M. | ||||||
Funding support | 1items
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![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 427.4 KB | Display | ![]() |
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PDB format | ![]() | 354.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 43.1 KB | Display | |
Data in CIF | ![]() | 64.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28048MC ![]() 8ee4C ![]() 8eeaC ![]() 8suxC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 53189.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 28136.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-ATP / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 6 ptuA form as a complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1832915 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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