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- PDB-8zyc: Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8zyc | |||||||||
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Title | Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex A | |||||||||
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![]() | TOXIN / RNase / Complex / Contact-dependent growth inhibition | |||||||||
Function / homology | ![]() tRNA-specific ribonuclease activity / cystathionine beta-synthase activity / cysteine synthase / cysteine synthase activity / other organism cell membrane / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / RNA endonuclease activity / toxin activity / host cell cytoplasm ...tRNA-specific ribonuclease activity / cystathionine beta-synthase activity / cysteine synthase / cysteine synthase activity / other organism cell membrane / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / RNA endonuclease activity / toxin activity / host cell cytoplasm / tRNA binding / Hydrolases; Acting on ester bonds / extracellular region / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
![]() | Feng, Z. / Yashiro, Y. / Tomita, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of activation of contact-dependent growth inhibition tRNase toxin by the amino acid biogenesis factor CysK in the bacterial competition system. Authors: Feng, Z. / Yashiro, Y. / Tomita, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.8 KB | Display | ![]() |
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PDB format | ![]() | 129.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 60561MC ![]() 8zydC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 34756.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 25181.250 Da / Num. of mol.: 1 / Mutation: H178A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q0T963, Hydrolases; Acting on ester bonds #3: RNA chain | | Mass: 25000.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Chemical | Has ligand of interest | N | |
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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 |
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Sample preparation
Component | Name: CysK in complex with CdiA-CT and tRNA. / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.11 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7 Details: 25mM Tris-HCl,50mM NaCl,2mM MgCl2, 10mM 2-mercaptoethanol | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7044 |
Image scans | Width: 4092 / Height: 5760 |
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Processing
EM software | Name: PHENIX / Version: 1.18.2_3874: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4707496 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115994 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 5J43 Accession code: 5J43 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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