+Open data
-Basic information
Entry | Database: PDB / ID: 8hr7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of RdrA-RdrB complex | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Cryoelectron microscopy / adenosine triphosphatase / adenosine deaminase | ||||||
Function / homology | deaminase activity / Adenosine/adenine deaminase / Metal-dependent hydrolase / P-loop containing nucleoside triphosphate hydrolase / Adenosine deaminase / Archaeal ATPase Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å | ||||||
Authors | Gao, Y. | ||||||
Funding support | China, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8hr7.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8hr7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8hr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hr7_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8hr7_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8hr7_validation.xml.gz | 373.6 KB | Display | |
Data in CIF | 8hr7_validation.cif.gz | 562.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/8hr7 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/8hr7 | HTTPS FTP |
-Related structure data
Related structure data | 34962MC 8hr8C 8hr9C 8hraC 8hrbC 8hrcC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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: Protein | Mass: 92216.953 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AW119_27895 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8E2SFD7 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RdrA-RdrB complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
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 |
---|---|
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 |
---|---|
3D reconstruction | Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23954 / Symmetry type: POINT |