Download MendeleyMechanism of activation of contact-dependent growth inhibition tRNase toxin by the amino acid biogenesis factor CysK in the bacterial competition system.
Feng, Z., Yashiro, Y., Tomita, K.To be published.
8ZYD
Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex B
- PDB DOI: https://doi.org/10.2210/pdb8ZYD/pdb
- NAKB: 8ZYD
- EM Map EMD-60562: EMDB EMDataResource
- Classification: TOXIN
- Organism(s): Escherichia coli, Escherichia coli 536
- Expression System: Escherichia coli BL21(DE3), Escherichia coli
- Mutation(s): No
- Deposited: 2024-06-17 Released: 2024-08-21
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.04 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cysteine synthase A | A, D [auth E] | 323 | Escherichia coli | Mutation(s): 0 Gene Names: cysK, Z3680, ECs3286 EC: 2.5.1.47 |  |
UniProt | |||||
Find proteins for P0ABK6 (Escherichia coli O157:H7) Explore P0ABK6 Go to UniProtKB: P0ABK6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0ABK6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| tRNA nuclease CdiA | 234 | Escherichia coli 536 | Mutation(s): 0 Gene Names: cdiA, ECP_4580 EC: 3.1 |  | |
UniProt | |||||
Find proteins for Q0T963 (Escherichia coli O6:K15:H31 (strain 536 / UPEC)) Explore Q0T963 Go to UniProtKB: Q0T963 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q0T963 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| tRNAIleGAU | 77 | Escherichia coli |  | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG Query on MG | E [auth B], F [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| LLP Query on LLP | A, D [auth E] | L-PEPTIDE LINKING | C14 H22 N3 O7 P |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.04 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | 1.18.2_3874: |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-08-21 Deposition Author(s): Feng, Z., Yashiro, Y., Tomita, K.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science (JSPS) | Japan | 18H03980 |
| Japan Society for the Promotion of Science (JSPS) | Japan | 23H00368 |
Revision History (Full details and data files)
- Version 1.0: 2024-08-21
Type: Initial release
