6CS8

High resolution crystal structure of FtsY-NG domain of E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report



Literature

Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics.

Faoro, C.Wilkinson-White, L.Kwan, A.H.Ataide, S.F.

(2018) PLoS One 13: e0200387-e0200387

  • DOI: 10.1371/journal.pone.0200387
  • Primary Citation of Related Structures:  
    6DLX, 6CQP, 6CS8, 6CVD

  • PubMed Abstract: 
  • Given the increasing incidence of antibiotic resistance, antibiotics that employ new strategies are urgently needed. Bacterial survival is dependent on proper function of the signal recognition particle (SRP) and its receptor (FtsY). A unique set of ...

    Given the increasing incidence of antibiotic resistance, antibiotics that employ new strategies are urgently needed. Bacterial survival is dependent on proper function of the signal recognition particle (SRP) and its receptor (FtsY). A unique set of interactions in FtsY:SRP-RNA represents a promising candidate for new antibiotic development as no antibiotic targets this complex and these interactions are functionally replaced by protein:protein interactions in eukaryotes. We used a Fragment Based Drug Design (FBDD) approach to search for new compounds that can bind FtsY, and have identified three lead fragments. In vitro and in vivo analyses have shown that despite a high micromolar binding affinity, one fragment has some antimicrobial properties. X-ray structures of E. coli FtsY:fragments reveal the fragments bind in the targeted RNA interaction site. Our results show that FBDD is a suitable approach for targeting FtsY:SRP-RNA for antibiotic development and opens the possibility of targeting protein:RNA interactions in general.


    Organizational Affiliation

    School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Signal recognition particle receptor FtsYA, B303Escherichia coli K-12Mutation(s): 0 
Gene Names: ftsYb3464JW3429
Find proteins for P10121 (Escherichia coli (strain K12))
Explore P10121 
Go to UniProtKB:  P10121
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F9Y
Query on F9Y

Download CCD File 
A, B
1H-indole-6-carbonitrile
C9 H6 N2
SZSZDBFJCQKTRG-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F9YKd:  100000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.541α = 90
b = 76.192β = 90.72
c = 107.978γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release