8ZYC

Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex A

• PDB DOI: https://doi.org/10.2210/pdb8ZYC/pdb
• NAKB: 8ZYC
• EM Map EMD-60561: 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 
• Deposition Author(s): Feng, Z., Yashiro, Y., Tomita, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Mechanism 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 119.74 kDa 
• Atom Count: 7,058 
• Modelled Residue Count: 801 
• Deposited Residue Count: 957 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

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 (PDB Primary Data), 4.5.1.5 (UniProt)
UniProt
Find proteins for P0ABK5 (Escherichia coli (strain K12)) Explore P0ABK5  Go to UniProtKB:  P0ABK5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA nuclease CdiA	B	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 ID: 3
Molecule	Chains	Length	Organism	Image
tRNAIleGAU	C	77	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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	A, D [auth E]	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2_3874:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Feng, Z., Yashiro, Y., Tomita, K.

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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  

• Version 1.0: 2024-08-21
  Type: Initial release