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- PDB-8v49: CryoEM structure of AriA (E393Q) sensory subunit -

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Basic information

Entry
Database: PDB / ID: 8v49
TitleCryoEM structure of AriA (E393Q) sensory subunit
ComponentsAriA antitoxin
KeywordsIMMUNE SYSTEM / Bacterial Defense system / Toxin-antitoxin system / AriAB / PARIS
Function / homologyADENOSINE-5'-TRIPHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli B185 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsDeep, A. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM144121 United States
CitationJournal: To Be Published
Title: CryoEM structure of AriA (E393Q) sensory subunit
Authors: Deep, A. / Corbett, K.D.
History
DepositionNov 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AriA antitoxin
B: AriA antitoxin
D: AriA antitoxin
C: AriA antitoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,6565
Polymers213,1484
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
AriA antitoxin


Mass: 53287.113 Da / Num. of mol.: 4 / Mutation: E393Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli B185 (bacteria) / Gene: ECDG_03487 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: D6IC77
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / 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: AriA hexamer / Type: COMPLEX / Details: AriA / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.30 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli B185 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta2 pLysS
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1250 mMSodium chlorideNaCl1
220 mMtris(hydroxymethyl)aminomethaneTris1
32 mM2-MercaptoethanolBME1
SpecimenConc.: 2 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: 95 % / Chamber temperature: 278 K

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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: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5174
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 20 eV

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5127 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106506 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 189.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004713066
ELECTRON MICROSCOPYf_angle_d0.857917583
ELECTRON MICROSCOPYf_chiral_restr0.05461933
ELECTRON MICROSCOPYf_plane_restr0.00592244
ELECTRON MICROSCOPYf_dihedral_angle_d12.45064869

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