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- PDB-8hrb: Structure of tetradecameric RdrA ring in RNA-loading state -

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Basic information

Entry
Database: PDB / ID: 8hrb
TitleStructure of tetradecameric RdrA ring in RNA-loading state
Components
  • Archaeal ATPase
  • RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
KeywordsIMMUNE SYSTEM / Cryoelectron microscopy / adenosine triphosphatase
Function / homologyP-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Archaeal ATPase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsGao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100984 China
CitationJournal: 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
DepositionDec 15, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Archaeal ATPase
K: Archaeal ATPase
L: Archaeal ATPase
M: Archaeal ATPase
P: Archaeal ATPase
Q: Archaeal ATPase
R: Archaeal ATPase
A: Archaeal ATPase
B: Archaeal ATPase
C: Archaeal ATPase
D: Archaeal ATPase
E: Archaeal ATPase
G: Archaeal ATPase
H: Archaeal ATPase
V: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
Z: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
X: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
W: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
Y: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
a: RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,542,16228
Polymers1,538,10420
Non-polymers4,0578
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Archaeal ATPase / RdrA


Mass: 107132.523 Da / Num. of mol.: 14
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: RNA chain
RNA (5'-R(*GP*UP*CP*CP*AP*GP*CP*GP*UP*CP*AP*UP*CP*GP*CP*UP*GP*GP*AP*C)-3')


Mass: 6374.831 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RdrA-RNA complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162577 / Symmetry type: POINT

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