+Open data
-Basic information
Entry | Database: PDB / ID: 8v46 | ||||||
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Title | CryoEM structure of AriA-AriB complex (Form I) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Bacterial Defense system / Toxin-antitoxin system / AriAB / PARIS | ||||||
Function / homology | ADENOSINE-5'-TRIPHOSPHATE / : / : Function and homology information | ||||||
Biological species | Escherichia coli B185 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å | ||||||
Authors | Deep, A. / Corbett, K.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2024 Title: Architecture and activation mechanism of the bacterial PARIS defence system Authors: Deep, A. / Liang, Q. / Enustun, E. / Pogliano, J. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v46.cif.gz | 371.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v46.ent.gz | 301.5 KB | Display | PDB format |
PDBx/mmJSON format | 8v46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v46_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8v46_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8v46_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 8v46_validation.cif.gz | 97.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/8v46 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/8v46 | HTTPS FTP |
-Related structure data
Related structure data | 42966MC 8v45C 8v47C 8v48C 8v49C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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: Protein | | Mass: 34749.578 Da / Num. of mol.: 1 / Mutation: E90A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli B185 (bacteria) / Gene: ECDG_03486 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: D6IC76 #3: Chemical | #4: Chemical | ChemComp-MG / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: AriAB complex / Type: COMPLEX / Details: AriA-AriB / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.33 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli B185 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Rosetta2 pLysS | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5058 |
EM imaging optics | Energyfilter name: TFS Selectris X / Energyfilter slit width: 20 eV |
-Processing
EM software | Name: PHENIX / Version: 1.21rc1_5127 / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132804 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 141.17 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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