+Open data
-Basic information
Entry | Database: PDB / ID: 8uy4 | |||||||||
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Title | Acinetobacter baumannii Tse15 Rhs effector | |||||||||
Components |
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Keywords | TOXIN / Rhs-effector / Rhs cargo effector / Type 6 secretion system effector / Acinetobacter baumannii toxin / Type VI secretion system / YD-repeat protein / T6SS. | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Acinetobacter baumannii AB307-0294 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Hayes, B.K. / Venugopal, H. / McGowan, S. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structure of a Rhs effector clade domain provides mechanistic insights into type VI secretion system toxin delivery Authors: Hayes, B.K. / Harper, M. / Venugopal, H. / Lewis, J.M. / Wright, A. / Lee, H.-C. / Steele, J.R. / Steer, D.L. / Schittenhelm, R.B. / Boyce, J.D. / McGowan, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uy4.cif.gz | 539.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uy4.ent.gz | 439 KB | Display | PDB format |
PDBx/mmJSON format | 8uy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uy4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8uy4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8uy4_validation.xml.gz | 50.7 KB | Display | |
Data in CIF | 8uy4_validation.cif.gz | 75.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/8uy4 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/8uy4 | HTTPS FTP |
-Related structure data
Related structure data | 42792MC 8uxtC 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: 182818.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria) Gene: ABBFA_02439 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A5K6CSR3 |
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#2: Protein/peptide | Mass: 2486.056 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria) Production host: Escherichia coli BL21 (bacteria) |
#3: Protein/peptide | Mass: 954.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria) Production host: Escherichia coli BL21 (bacteria) |
#4: Protein/peptide | Mass: 3762.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria) Production host: Escherichia coli BL21 (bacteria) |
#5: Protein/peptide | Mass: 2060.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria) Production host: Escherichia coli BL21 (bacteria) |
Has protein modification | N |
Sequence details | Tse15 toxin peptides are fragments unregistered to sample sequence due to poor density. |
-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: Recombinant Tse15 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.183 MDa / Experimental value: NO |
Source (natural) | Organism: Acinetobacter baumannii AB307-0294 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) |
Buffer solution | pH: 8 / Details: 50 mM Hepes pH 8.0; 300 mM NaCl |
Specimen | Conc.: 3 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: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 455508 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132696 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: Initial fitting with done using UCSF Chimera using fit map. | ||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||
Refine LS restraints |
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