6U33 | pdb_00006u33

Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus

• PDB DOI: https://doi.org/10.2210/pdb6U33/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli K-12
• Mutation(s): No 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2019-08-21 Released: 2020-03-25 
• Deposition Author(s): Liu, J., Kozhaya, L., Torres, V.J., Unutmaz, D., Lu, M.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Structure-based discovery of a small-molecule inhibitor of methicillin-resistantStaphylococcus aureusvirulence.

Liu, J., Kozhaya, L., Torres, V.J., Unutmaz, D., Lu, M.

(2020) J Biological Chem 295: 5944-5959

• PubMed: 32179646 
• DOI: https://doi.org/10.1074/jbc.RA120.012697
• Primary Citation Related Structures: 
  6U2S, 6U33, 6U3F, 6U3T, 6U3Y, 6U49, 6U4P


• PubMed Abstract: 
  

  The rapid emergence and dissemination of methicillin-resistant Staphylococcus aureus (MRSA) strains poses a major threat to public health. MRSA possesses an arsenal of secreted host-damaging virulence factors that mediate pathogenicity and blunt immune defenses. Panton-Valentine leukocidin (PVL) and α-toxin are exotoxins that create lytic pores in the host cell membrane. They are recognized as being important for the development of invasive MRSA infections and are thus potential targets for antivirulence therapies. Here, we report the high-resolution X-ray crystal structures of both PVL and α-toxin in their soluble, monomeric, and oligomeric membrane-inserted pore states in complex with n -tetradecylphosphocholine (C ₁₄ PC). The structures revealed two evolutionarily conserved phosphatidylcholine-binding mechanisms and their roles in modulating host cell attachment, oligomer assembly, and membrane perforation. Moreover, we demonstrate that the soluble C ₁₄ PC compound protects primary human immune cells in vitro against cytolysis by PVL and α-toxin and hence may serve as the basis for the development of an antivirulence agent for managing MRSA infections.

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Organizational Affiliation: 
• Public Health Research Institute, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103.
Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032.
Department of Microbiology, New York University School of Medicine, New York, New York 10016.
Public Health Research Institute, Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.26 kDa 
• Atom Count: 2,598 
• Modeled Residue Count: 296 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bi-component leukocidin LukED subunit D	A	301	Staphylococcus aureus	Mutation(s): 0  Gene Names: lukNF, lukD, BTN44_02870, EP54_14125, EQ90_10595, ER624_13605, HMPREF3211_01500, NCTC10654_01892, NCTC13131_06007, RK64_09800 Membrane Entity: Yes
UniProt
Find proteins for Q2FXB1 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXB1  Go to UniProtKB:  Q2FXB1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.611	α = 90
b = 48.732	β = 120.85
c = 66.731	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Liu, J., Kozhaya, L., Torres, V.J., Unutmaz, D., Lu, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2020-04-01
  Changes: Database references
• Version 1.2: 2020-05-13
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description