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- PDB-8ux9: Asymmetric unit of the PARIS Immune Complex at 3.2 Angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 8ux9
TitleAsymmetric unit of the PARIS Immune Complex at 3.2 Angstrom Resolution
Components
  • AriA
  • AriB
KeywordsIMMUNE SYSTEM / PARIS / AriA / AriB / DUF4435
Function / homologyPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / :
Function and homology information
Biological speciesEscherichia coli B185 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBurman, N.B. / Henriques, W. / Wilkinson, R. / Graham, A. / Wiedenheft, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134867 United States
CitationJournal: Nature / Year: 2024
Title: A virally encoded tRNA neutralizes the PARIS antiviral defence system.
Authors: Nathaniel Burman / Svetlana Belukhina / Florence Depardieu / Royce A Wilkinson / Mikhail Skutel / Andrew Santiago-Frangos / Ava B Graham / Alexei Livenskyi / Anna Chechenina / Natalia ...Authors: Nathaniel Burman / Svetlana Belukhina / Florence Depardieu / Royce A Wilkinson / Mikhail Skutel / Andrew Santiago-Frangos / Ava B Graham / Alexei Livenskyi / Anna Chechenina / Natalia Morozova / Trevor Zahl / William S Henriques / Murat Buyukyoruk / Christophe Rouillon / Baptiste Saudemont / Lena Shyrokova / Tatsuaki Kurata / Vasili Hauryliuk / Konstantin Severinov / Justine Groseille / Agnès Thierry / Romain Koszul / Florian Tesson / Aude Bernheim / David Bikard / Blake Wiedenheft / Artem Isaev /
Abstract: Viruses compete with each other for limited cellular resources, and some deliver defence mechanisms that protect the host from competing genetic parasites. The phage antirestriction induced system ...Viruses compete with each other for limited cellular resources, and some deliver defence mechanisms that protect the host from competing genetic parasites. The phage antirestriction induced system (PARIS) is a defence system, often encoded in viral genomes, that is composed of a 55 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB). However, the mechanism by which AriA and AriB function in phage defence is unknown. Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex. We use cryo-electron microscopy to determine the structure of this complex, thereby explaining how six molecules of AriA assemble into a propeller-shaped scaffold that coordinates three subunits of AriB. ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving host lysine transfer RNA. Phage T5 subverts PARIS immunity through expression of a lysine transfer RNA variant that is not cleaved by PARIS, thereby restoring viral infection. Collectively, these data explain how AriA functions as an ATP-dependent sensor that detects viral proteins and activates the AriB toxin. PARIS is one of an emerging set of immune systems that form macromolecular complexes for the recognition of foreign proteins, rather than foreign nucleic acids.
History
DepositionNov 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AriB
B: AriA
C: AriA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,5375
Polymers142,4903
Non-polymers1,0462
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein AriB


Mass: 35849.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AriB, DUF4435 and TOPRIM-containing protein and effector of the PARIS immune complex.
Source: (gene. exp.) Escherichia coli B185 (bacteria) / Gene: ECDG_03486 / Plasmid: pRSF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6IC76
#2: Protein AriA


Mass: 53320.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: AriA, ABC-ATPase, Sensor of PARIS-mediated immunity
Source: (gene. exp.) Escherichia coli B185 (bacteria) / Gene: ECDG_03487 / Plasmid: pRSF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6IC77
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationN

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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: Asymmetric unit of the PARIS immune complex with AriA bound to two molecules of ATPGS and inactive AriB effector.
Type: COMPLEX
Details: Map generated by local refinement of one asymmetric unit of the intact PARIS complex.
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli B185 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pRSF-Duet
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris1
2150 mMSodium ChlorideNaCl1
35 %Glycerol1
41 mMATP gamma S1
SpecimenConc.: 5.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 297 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 56.42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7340

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3.1particle selection
2SerialEMimage acquisition
4cryoSPARC4.3.1CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARC4.3.1initial Euler assignment
10cryoSPARC4.3.1final Euler assignment
11cryoSPARC4.3.1classification
12cryoSPARC4.3.13D reconstruction
13PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 532010 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037944
ELECTRON MICROSCOPYf_angle_d0.50110858
ELECTRON MICROSCOPYf_dihedral_angle_d7.5281201
ELECTRON MICROSCOPYf_chiral_restr0.0451303
ELECTRON MICROSCOPYf_plane_restr0.0051368

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