8FR3 | pdb_00008fr3

E. coli EF-Tu in complex with KKL-55

• PDB DOI: https://doi.org/10.2210/pdb8FR3/pdb

• Classification: TRANSLATION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-06 Released: 2023-09-20 
• Deposition Author(s): Nguyen, H.A., Kuzmishin Nagy, A.B., Dunham, C.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Antibiotic that inhibits trans -translation blocks binding of EF-Tu to tmRNA but not to tRNA.

Marathe, N., Nguyen, H.A., Alumasa, J.N., Kuzmishin Nagy, A.B., Vazquez, M., Dunham, C.M., Keiler, K.C.

(2023) mBio 14: e0146123-e0146123

• PubMed: 37681945 
• DOI: https://doi.org/10.1128/mbio.01461-23
• Primary Citation Related Structures: 
  8FR3


• PubMed Abstract: 
  

  Elongation factor thermo-unstable (EF-Tu) is a universally conserved translation factor that mediates productive interactions between tRNAs and the ribosome. In bacteria, EF-Tu also delivers transfer-messenger RNA (tmRNA)-SmpB to the ribosome during trans -translation. We report the first small molecule, KKL-55, that specifically inhibits EF-Tu activity in trans -translation without affecting its activity in normal translation. KKL-55 has broad-spectrum antibiotic activity, suggesting that compounds targeted to the tmRNA-binding interface of EF-Tu could be developed into new antibiotics to treat drug-resistant infections.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania, USA.
Department of Chemistry, Emory University , Atlanta, Georgia, USA.
Emory Antibiotic Resistance Center (ARC), Emory University , Atlanta, Georgia, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.03 kDa 
• Atom Count: 6,018 
• Modeled Residue Count: 770 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor Tu	A, B	402	Escherichia coli K-12	Mutation(s): 0  Gene Names: tuf EC: 3.6.5.3
UniProt
Find proteins for P0CE47 (Escherichia coli (strain K12)) Explore P0CE47  Go to UniProtKB:  P0CE47

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], G [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
Y7C (Subject of Investigation/LOI)	E [auth A]	3-chloro-N-(1-propyl-1H-tetrazol-5-yl)benzamide C11 H12 Cl N5 O IBRCUOMIAFDQTM-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.385	α = 107.67
b = 65.222	β = 98.79
c = 70.559	γ = 107.08

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Nguyen, H.A., Kuzmishin Nagy, A.B., Dunham, C.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	2R01GM121650

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Database references