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- EMDB-42719: Asymmetric unit of the PARIS Immune Complex at 3.2 Angstrom Resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-42719
TitleAsymmetric unit of the PARIS Immune Complex at 3.2 Angstrom Resolution
Map data
Sample
  • Complex: Asymmetric unit of the PARIS immune complex with AriA bound to two molecules of ATPGS and inactive AriB effector.
    • Protein or peptide: AriB
    • Protein or peptide: AriA
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsPARIS / AriA / AriB / DUF4435 / IMMUNE SYSTEM
Function / homology: / :
Function and homology information
Biological speciesEscherichia coli B185 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBurman NB / Henriques W / Wilkinson R / Graham A / Wiedenheft B
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42719.png

Downloads & links

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Map

FileDownload / File: emd_42719.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 331.2 Å		1.1 Å/pix.
x 300 pix.
= 331.2 Å		1.1 Å/pix.
x 300 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.104 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0017235558 - 1.7099967
Average (Standard dev.)0.0005765565 (±0.016854938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 331.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Asymmetric unit of the PARIS immune complex with AriA bound to tw...

EntireName: Asymmetric unit of the PARIS immune complex with AriA bound to two molecules of ATPGS and inactive AriB effector.
Components
  • Complex: Asymmetric unit of the PARIS immune complex with AriA bound to two molecules of ATPGS and inactive AriB effector.
    • Protein or peptide: AriB
    • Protein or peptide: AriA
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: Asymmetric unit of the PARIS immune complex with AriA bound to tw...

SupramoleculeName: Asymmetric unit of the PARIS immune complex with AriA bound to two molecules of ATPGS and inactive AriB effector.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Map generated by local refinement of one asymmetric unit of the intact PARIS complex.
Source (natural)Organism: Escherichia coli B185 (bacteria)

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Macromolecule #1: AriB

MacromoleculeName: AriB / type: protein_or_peptide / ID: 1
Details: AriB, DUF4435 and TOPRIM-containing protein and effector of the PARIS immune complex.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli B185 (bacteria)
Molecular weightTheoretical: 35.849762 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSCAYTIDS YITLLTMSSK KRLLVEGRHD RSHLYQLIYK FNPASKVKID TAQDIKASDK AMSKNNRLKI ETIHSKVKGK DNISFLCDR EFREFAFNDQ IEDLLNSHYC DDSLYWTLGH SLENYFFNPS IIIDAFQFLS PSEYKYKAIE LFSELISSSF A VLAAVSLA ...String:
MSSCAYTIDS YITLLTMSSK KRLLVEGRHD RSHLYQLIYK FNPASKVKID TAQDIKASDK AMSKNNRLKI ETIHSKVKGK DNISFLCDR EFREFAFNDQ IEDLLNSHYC DDSLYWTLGH SLENYFFNPS IIIDAFQFLS PSEYKYKAIE LFSELISSSF A VLAAVSLA AKDIDKAGLP AALIDWKDIV INDGTIKLIR RDSYDIDSAC VDSFFNAFDA VLPRVIASDV GICSRVVRGH TG ILLLQKL FSACLYYVGR EDDALQADSS ANYFCNLSEL SLTTALAESW VRKIGVLEDV YFPDSLLKNI EWSHPQFEK

UniProtKB: UNIPROTKB: D6IC76

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Macromolecule #2: AriA

MacromoleculeName: AriA / type: protein_or_peptide / ID: 2
Details: AriA, ABC-ATPase, Sensor of PARIS-mediated immunity
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli B185 (bacteria)
Molecular weightTheoretical: 53.320164 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAIRTISKIE LSKIHNRYNL TVDFFNDLNV IHGKNGAGKS TLIHVIANIV NGDFIRFAFL IFEEIKATYS DGLKIVIRRD KIDEQSFIS VTLSNGKYIK FAVGEAMATV REIESERHLR ERDVKSMLAM DIDKFVKENE LQKVRASYFP AFRTMLEAWS S SSDVGYER ...String:
MAIRTISKIE LSKIHNRYNL TVDFFNDLNV IHGKNGAGKS TLIHVIANIV NGDFIRFAFL IFEEIKATYS DGLKIVIRRD KIDEQSFIS VTLSNGKYIK FAVGEAMATV REIESERHLR ERDVKSMLAM DIDKFVKENE LQKVRASYFP AFRTMLEAWS S SSDVGYER RVIRSSFYNR KASAFARELF GQFLPSINYP SPMEIEDRLR EEIRRAQLGI AAYESRTFSE SFVKVFSALF DN SSVEGEI TGELLKEIEG LAIAQDSSIK NGYYAEYSKV YEEIRSLINR NLKGKVENSV SGALVVYRDA LRDRQDYQEK AFS EIDNYM SSVNSFLEDK EMAYDFDLRR KYPKVGLKFP DGSWSPIRVL SSGERQLLTM LYAASKMGDD AIVLIDEPEI SLHI DWQED LLKRMLSQLS GRQIIVCTHS PSIATGYEDF MINISPEFIS SRDNDNHKDS EEMEEDESL

UniProtKB: UNIPROTKB: D6IC77

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5.8 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMSodium ChlorideNaCl
5.0 %Glycerol
1.0 mMATP gamma S
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7340 / Average electron dose: 56.42 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 532010
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

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

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