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- EMDB-43104: PARIS immune complex with AriB subunits in the trans arrangement. -

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Basic information

Entry
Database: EMDB / ID: EMD-43104
TitlePARIS immune complex with AriB subunits in the trans arrangement.
Map dataSharpened map of fully assembled PARIS complex with AriB subunits in Trans arrangement.
Sample
  • Complex: PARIS immune complex in the assembled state with AriB subunits in a C3-symmetric arrangement.
    • Protein or peptide: AriA, ABC ATPase and sensor of PARIS immunity
    • Protein or peptide: AriB, DUF4435 and TOPRIM containing nuclease, effector of the PARIS immune system.
KeywordsPARIS / AriA / AriB / DUF4435 / IMMUNE SYSTEM
Biological speciesEscherichia coli B185 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 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
DepositionDec 11, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43104.png

Downloads & links

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Map

FileDownload / File: emd_43104.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of fully assembled PARIS complex with AriB subunits in Trans arrangement.
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: 0.15
Minimum - Maximum-0.0007912863 - 1.8341613
Average (Standard dev.)0.0028681622 (±0.037053965)
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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Half map: Half Map A used for sharpening and gold standard FSC calculation

Fileemd_43104_half_map_1.map
AnnotationHalf Map A used for sharpening and gold standard FSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B used for sharpening and gold standard FSC calculation

Fileemd_43104_half_map_2.map
AnnotationHalf Map B used for sharpening and gold standard FSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PARIS immune complex in the assembled state with AriB subunits in...

EntireName: PARIS immune complex in the assembled state with AriB subunits in a C3-symmetric arrangement.
Components
  • Complex: PARIS immune complex in the assembled state with AriB subunits in a C3-symmetric arrangement.
    • Protein or peptide: AriA, ABC ATPase and sensor of PARIS immunity
    • Protein or peptide: AriB, DUF4435 and TOPRIM containing nuclease, effector of the PARIS immune system.

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Supramolecule #1: PARIS immune complex in the assembled state with AriB subunits in...

SupramoleculeName: PARIS immune complex in the assembled state with AriB subunits in a C3-symmetric arrangement.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli B185 (bacteria)

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Macromolecule #1: AriA, ABC ATPase and sensor of PARIS immunity

MacromoleculeName: AriA, ABC ATPase and sensor of PARIS immunity / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli B185 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAIRTISKIE LSKIHNRYNL TVDFFNDLNV IHGKNGAGKS TLIHVIANIV NGDFIRFAFL IFEEIKATYS DGLKIVIRRD KIDEQSFISV TLSNGKYIKF AVGEAMATVR EIESERHLRE RDVKSMLAMD IDKFVKENEL QKVRASYFPA FRTMLEAWSS SSDVGYERRV ...String:
MAIRTISKIE LSKIHNRYNL TVDFFNDLNV IHGKNGAGKS TLIHVIANIV NGDFIRFAFL IFEEIKATYS DGLKIVIRRD KIDEQSFISV TLSNGKYIKF AVGEAMATVR EIESERHLRE RDVKSMLAMD IDKFVKENEL QKVRASYFPA FRTMLEAWSS SSDVGYERRV IRSSFYNRKA SAFARELFGQ FLPSINYPSP MEIEDRLREE IRRAQLGIAA YESRTFSESF VKVFSALFDN SSVEGEITGE LLKEIEGLAI AQDSSIKNGY YAEYSKVYEE IRSLINRNLK GKVENSVSGA LVVYRDALRD RQDYQEKAFS EIDNYMSSVN SFLEDKEMAY DFDLRRKYPK VGLKFPDGSW SPIRVLSSGE RQLLTMLYAA SKMGDDAIVL IDEPEISLHI DWQEDLLKRM LSQLSGRQII VCTHSPSIAT GYEDFMINIS PEFISSRDND NHKDSEEMEE DESL

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Macromolecule #2: AriB, DUF4435 and TOPRIM containing nuclease, effector of the PAR...

MacromoleculeName: AriB, DUF4435 and TOPRIM containing nuclease, effector of the PARIS immune system.
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli B185 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSCAYTIDS YITLLTMSSK KRLLVEGRHD RSHLYQLIYK FNPASKVKID TAQDIKASDK AMSKNNRLKI ETIHSKVKGK DNISFLCDRE FREFAFNDQI EDLLNSHYCD DSLYWTLGHS LENYFFNPSI IIDAFQFLSP SEYKYKAIEL FSELISSSFA VLAAVSLAAK ...String:
MSSCAYTIDS YITLLTMSSK KRLLVEGRHD RSHLYQLIYK FNPASKVKID TAQDIKASDK AMSKNNRLKI ETIHSKVKGK DNISFLCDRE FREFAFNDQI EDLLNSHYCD DSLYWTLGHS LENYFFNPSI IIDAFQFLSP SEYKYKAIEL FSELISSSFA VLAAVSLAAK DIDKAGLPAA LIDWKDIVIN DGTIKLIRRD SYDIDSACVD SFFNAFDAVL PRVIASDVGI CSRVVRGHTG ILLLQKLFSA CLYYVGREDD ALQADSSANY FCNLSELSLT TALAESWVRK IGVLEDVYFP DSLLKNIEWS HPQFEK

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 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: 56.38 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: 2.5 µm / Nominal defocus min: 0.8 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

Particle selectionNumber selected: 4078384
Details: Particles Extracted for initial classification Template for particle picking generated from processing a 200 micrograph subset of the data using the blob picker. A volume corresponding to ...Details: Particles Extracted for initial classification Template for particle picking generated from processing a 200 micrograph subset of the data using the blob picker. A volume corresponding to the assembled PARIS complex was identified and Alphafold2 models were docked into the map. ChimeraX's molmap command was used to generate a 20 Angstrom lowpass filtered volume of the docked Alphafold2 models and imported to Cryosparc for template generation.
Startup modelType of model: NONE
Details: Multiclass ab-initio reconstructions were used to sort particle images and obtain a consensus refinement.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.41) / Software - details: Non-Uniform Refinement
Details: Resolution Estimate from cryoSPARC's own implementation.
Number images used: 122866
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.41) / Software - details: Ab-Initio Reconstruction
Details: A three class ab-initio reconstruction was used to remove junk classes.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.41) / Software - details: Non-Uniform Refinement
Details: After multiple rounds of Ab-initio reconstruction and heterogenous refinement, a 532,010 particle stack was isolated that corresponded to the fully assembled PARIS complex. In this volume, ...Details: After multiple rounds of Ab-initio reconstruction and heterogenous refinement, a 532,010 particle stack was isolated that corresponded to the fully assembled PARIS complex. In this volume, one asymmetric unit of the complex is well-aligned, while in the others, the AriB subunits are present in two, mutually exclusive orientations. This mixture of particles in the assembled PARIS complex correspond to the Cis and Trans arrangements of the complex and as such, the particles were further sorted using focused 3-D classification to isolate the two structural isomers of the complex.
Final 3D classificationNumber classes: 2 / Avg.num./class: 136219 / Software - Name: cryoSPARC (ver. 4.41) / Software - details: Focused 3-D Classification
Details: From the 532,010 particle stack identified above, multiple rounds of focused 3-D Classification were used to isolate particle images of the PARIS complex with AriB subunits in the trans arrangement.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8ux9


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The initial model consisted of 3 copies of the PDB entry 8UX9
DetailsRigid body fitting was done using the fitmap command in ChimeraX to dock 3 copies of the experimentally determined structure of the asymmetric unit into the density map of the fully assembled complex.
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 158.6 / Target criteria: Cross-correlation coefficient

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