+Open data
-Basic information
Entry | Database: PDB / ID: 8hr8 | ||||||
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Title | Structure of heptameric RdrA ring | ||||||
Components | Archaeal ATPase | ||||||
Keywords | IMMUNE SYSTEM / Cryoelectron microscopy / adenosine triphosphatase | ||||||
Function / homology | P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-TRIPHOSPHATE / Archaeal ATPase Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Gao, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell / Year: 2023 Title: Molecular basis of RADAR anti-phage supramolecular assemblies. Authors: Yina Gao / Xiu Luo / Peipei Li / Zhaolong Li / Feng Ye / Songqing Liu / Pu Gao / Abstract: Adenosine-to-inosine RNA editing has been proposed to be involved in a bacterial anti-phage defense system called RADAR. RADAR contains an adenosine triphosphatase (RdrA) and an adenosine deaminase ...Adenosine-to-inosine RNA editing has been proposed to be involved in a bacterial anti-phage defense system called RADAR. RADAR contains an adenosine triphosphatase (RdrA) and an adenosine deaminase (RdrB). Here, we report cryo-EM structures of RdrA, RdrB, and currently identified RdrA-RdrB complexes in the presence or absence of RNA and ATP. RdrB assembles into a dodecameric cage with catalytic pockets facing outward, while RdrA adopts both autoinhibited tetradecameric and activation-competent heptameric rings. Structural and functional data suggest a model in which RNA is loaded through the bottom section of the RdrA ring and translocated along its inner channel, a process likely coupled with ATP-binding status. Intriguingly, up to twelve RdrA rings can dock one RdrB cage with precise alignments between deaminase catalytic pockets and RNA-translocation channels, indicative of enzymatic coupling of RNA translocation and deamination. Our data uncover an interesting mechanism of enzymatic coupling and anti-phage defense through supramolecular assemblies. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hr8.cif.gz | 1003 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hr8.ent.gz | 830.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hr8_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8hr8_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8hr8_validation.xml.gz | 150.5 KB | Display | |
Data in CIF | 8hr8_validation.cif.gz | 225.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/8hr8 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/8hr8 | HTTPS FTP |
-Related structure data
Related structure data | 34963MC 8hr7C 8hr9C 8hraC 8hrbC 8hrcC 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: Protein | Mass: 107132.523 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AW119_27900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H9B1T2 #2: 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 |
-Sample preparation
Component | Name: RdrA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
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: 1500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108795 / Symmetry type: POINT |