43YH | pdb_000043yh

Cryo-EM structure of enterohemorrhagic Escherichia coli CdiA-CT:Tu(GTP):Ts:tRNA complex

• PDB DOI: https://doi.org/10.2210/pdb43YH/pdb
• EM Map EMD-82388: EMDB EMDataResource

• Classification: TOXIN
• Organism(s): Escherichia coli, Escherichia coli O157:H7 str. EC869
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2026-07-21 Released: 2026-11-11 
• Deposition Author(s): Zhaohang, F., Tomita, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Repurposing translation factors into a composite tRNA-processing enzyme

Zhaohang, F., Tomita, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 112.52 kDa 
• Atom Count: 7,313 
• Modeled Residue Count: 818 
• Deposited Residue Count: 883 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor Ts,Elongation factor Tu 2,tRNA nuclease CdiA	B [auth A]	808	Escherichia coli, Escherichia coli O157:H7 str. EC869	Mutation(s): 1  Gene Names: tsf, EcE24377A_0174, tuf2, EcHS_A4213, cdiA1, ECH7EC869_5848 EC: 3.6.5.3 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for A7ZHR0 (Escherichia coli O139:H28 (strain E24377A / ETEC)) Explore A7ZHR0  Go to UniProtKB:  A7ZHR0
Find proteins for A8A779 (Escherichia coli O9:H4 (strain HS)) Explore A8A779  Go to UniProtKB:  A8A779
Find proteins for B3BM48 (Escherichia coli O157:H7 (strain EC869)) Explore B3BM48  Go to UniProtKB:  B3BM48
UniProt Groups	B3BM48A7ZHR0A8A779

Entity ID: 1
Molecule	Chains	Length	Organism	Image
tRNAGlnCUG	A [auth t]	75	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP (Subject of Investigation/LOI)	G [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	C [auth t], D [auth t], E [auth t], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	5.0.6
MODEL REFINEMENT	PHENIX	1.18.2_3874:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-11 
Deposition Author(s): Zhaohang, F., Tomita, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	26H02359
Japan Society for the Promotion of Science (JSPS)	Japan	23H00368
Japan Society for the Promotion of Science (JSPS)	Japan	18H03980
Japan Agency for Medical Research and Development (AMED)	Japan	JP26ama121002

Revision History  

• Version 1.0: 2026-11-11
  Type: Initial release