3ROH | pdb_00003roh

Crystal Structure of Leukotoxin (LukE) from Staphylococcus aureus subsp. aureus COL.

• PDB DOI: https://doi.org/10.2210/pdb3ROH/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-25 Released: 2011-05-04 
• Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.224 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of the components of the Staphylococcus aureus leukotoxin ED.

Nocadello, S., Minasov, G., Shuvalova, L., Dubrovska, I., Sabini, E., Bagnoli, F., Grandi, G., Anderson, W.F.

(2016) Acta Crystallogr D Biol Crystallogr 72: 113-120

• PubMed: 26894539 
• DOI: https://doi.org/10.1107/S2059798315023207
• Primary Citation Related Structures: 
  3ROH, 4Q7G


• PubMed Abstract: 
  

  Staphylococcal leukotoxins are a family of β-barrel, bicomponent, pore-forming toxins with membrane-damaging functions. These bacterial exotoxins share sequence and structural homology and target several host-cell types. Leukotoxin ED (LukED) is one of these bicomponent pore-forming toxins that Staphylococcus aureus produces in order to suppress the ability of the host to contain the infection. The recent delineation of the important role that LukED plays in S. aureus pathogenesis and the identification of its protein receptors, combined with its presence in S. aureus methicillin-resistant epidemic strains, establish this leukocidin as a possible target for the development of novel therapeutics. Here, the crystal structures of the water-soluble LukE and LukD components of LukED have been determined. The two structures illustrate the tertiary-structural variability with respect to the other leukotoxins while retaining the conservation of the residues involved in the interaction of the protomers in the bipartite leukotoxin in the pore complex.

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Organizational Affiliation: 
• Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
Novartis Vaccines and Diagnostics, Research Centre, Siena, Italy.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 37.26 kDa 
• Atom Count: 2,286 
• Modeled Residue Count: 282 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucotoxin LukEv	A	329	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: HMPREF0773_11197, lukE, lukEv, SAOUHSC_01955
UniProt
Find proteins for Q2FXB0 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXB0  Go to UniProtKB:  Q2FXB0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	B [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.224 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33roh

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.904	α = 90
b = 133.904	β = 90
c = 64.473	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-03-02
  Changes: Database references
• Version 1.3: 2016-03-16
  Changes: Source and taxonomy
• Version 1.4: 2017-11-08
  Changes: Refinement description
• Version 1.5: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description