+Open data
-Basic information
Entry | Database: PDB / ID: 8i88 | ||||||
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Title | Cryo-EM structure of TIR-APAZ/Ago-gRNA complex | ||||||
Components |
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Keywords | VIRAL PROTEIN/ANTIVIRAL PROTEIN / a protein complex / VIRAL PROTEIN-ANTIVIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Maribacter polysiphoniae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Zhang, H. / Li, Z. / Yu, G.M. / Li, X.Z. / Wang, X.S. | ||||||
Funding support | 1items
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Citation | Journal: Cell Res / Year: 2023 Title: Structural insights into mechanisms of Argonaute protein-associated NADase activation in bacterial immunity. Authors: Xiaoshen Wang / Xuzichao Li / Guimei Yu / Lingling Zhang / Chendi Zhang / Yong Wang / Fumeng Liao / Yanan Wen / Hang Yin / Xiang Liu / Yong Wei / Zhuang Li / Zengqin Deng / Heng Zhang / Abstract: Nicotinamide adenine dinucleotide (NAD) is a central metabolite in cellular processes. Depletion of NAD has been demonstrated to be a prevalent theme in both prokaryotic and eukaryotic immune ...Nicotinamide adenine dinucleotide (NAD) is a central metabolite in cellular processes. Depletion of NAD has been demonstrated to be a prevalent theme in both prokaryotic and eukaryotic immune responses. Short prokaryotic Argonaute proteins (Agos) are associated with NADase domain-containing proteins (TIR-APAZ or SIR2-APAZ) encoded in the same operon. They confer immunity against mobile genetic elements, such as bacteriophages and plasmids, by inducing NAD depletion upon recognition of target nucleic acids. However, the molecular mechanisms underlying the activation of such prokaryotic NADase/Ago immune systems remain unknown. Here, we report multiple cryo-EM structures of NADase/Ago complexes from two distinct systems (TIR-APAZ/Ago and SIR2-APAZ/Ago). Target DNA binding triggers tetramerization of the TIR-APAZ/Ago complex by a cooperative self-assembly mechanism, while the heterodimeric SIR2-APAZ/Ago complex does not assemble into higher-order oligomers upon target DNA binding. However, the NADase activities of these two systems are unleashed via a similar closed-to-open transition of the catalytic pocket, albeit by different mechanisms. Furthermore, a functionally conserved sensor loop is employed to inspect the guide RNA-target DNA base pairing and facilitate the conformational rearrangement of Ago proteins required for the activation of these two systems. Overall, our study reveals the mechanistic diversity and similarity of Ago protein-associated NADase systems in prokaryotic immune response. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i88.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i88.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 8i88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i88_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8i88_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8i88_validation.xml.gz | 37 KB | Display | |
Data in CIF | 8i88_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/8i88 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/8i88 | HTTPS FTP |
-Related structure data
Related structure data | 35241MC 8i87C 8in8C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: RNA chain | Mass: 629.454 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 58091.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Gene: LX92_01809 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A316E3U6 |
#3: Protein | Mass: 53270.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Maribacter polysiphoniae (bacteria) / Gene: LX92_01810 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A316E683 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of TIR-APAZ/Ago-gRNA complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Maribacter polysiphoniae (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_4674: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200000 / Symmetry type: POINT | ||||||||||||||||||||||||
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