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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: To Be Published
Title: Activation of the PARIS immune complex results in tRNA cleavage and can be subverted by viral tRNAs
Authors: Burman, N.B. / Belukhina, S. / Depardieu, F. / Wilkinson, R. / Skutel, M. / Graham, A. / Livenskyi, A. / Chechenina, A. / Morozova, N. / Zahl, T. / Henriques, W. / Buyukyoruk, M. / Rouillon, ...Authors: Burman, N.B. / Belukhina, S. / Depardieu, F. / Wilkinson, R. / Skutel, M. / Graham, A. / Livenskyi, A. / Chechenina, A. / Morozova, N. / Zahl, T. / Henriques, W. / Buyukyoruk, M. / Rouillon, C. / Shyrokova, O. / Suzuki, T. / Hauryliuk, V. / Severinov, K. / Groseille, J. / Thierry, A. / Koszul, R. / Tesson, F. / Bernheim, A. / Bikard, D. / Wiedenheft, B. / Isaev, A.
History
DepositionNov 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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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

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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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