Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.00 kDa 
• Atom Count: 2579 
• Residue Count: 334 
• Unique protein chains: 1

4F24

Crystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus ClfB

• DOI: 10.2210/pdb4F24/pdb

• Classification: CELL ADHESION
• Organism(s): Staphylococcus aureus subsp. aureus MRSA252
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-07 Released: 2012-08-08 
• Deposition Author(s): Yang, M.J., Xiang, H., Wang, J.W., Liu, B., Chen, Y.G., Liu, L., Deng, X.M., Feng, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.289 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

Literature

Crystal Structures Reveal the Multi-Ligand Binding Mechanism of Staphylococcus aureus ClfB

Xiang, H., Feng, Y., Wang, J.W., Liu, B., Chen, Y.G., Liu, L., Deng, X.M., Yang, M.J.

(2012) PLoS Pathog 8: e1002751-e1002751

• PubMed: 22719251 
• DOI: 10.1371/journal.ppat.1002751
• Primary Citation of Related Structures:  
  4F1Z, 4F20, 4F24, 4F27


• PubMed Abstract: 
  

Staphylococcus aureus (S. aureus) pathogenesis is a complex process involving a diverse array of extracellular and cell wall components. ClfB, an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules) family surface protein, described as a fibrinogen-binding clumping factor, is a key determinant of S. aureus nasal colonization, but the molecular basis for ClfB-ligand recognition remains unknown. In this study, we solved the crystal structures of apo-ClfB and its complexes with fibrinogen α (Fg α) and cytokeratin 10 (CK10) peptides. Structural comparison revealed a conserved glycine-serine-rich (GSR) ClfB binding motif (GSSGXGXXG) within the ligands, which was also found in other human proteins such as Engrailed protein, TCF20 and Dermokine proteins. Interaction between Dermokine and ClfB was confirmed by subsequent binding assays. The crystal structure of ClfB complexed with a 15-residue peptide derived from Dermokine revealed the same peptide binding mode of ClfB as identified in the crystal structures of ClfB-Fg α and ClfB-CK10. The results presented here highlight the multi-ligand binding property of ClfB, which is very distinct from other characterized MSCRAMMs to-date. The adherence of multiple peptides carrying the GSR motif into the same pocket in ClfB is reminiscent of MHC molecules. Our results provide a template for the identification of other molecules targeted by S. aureus during its colonization and infection. We propose that other MSCRAMMs like ClfA and SdrG also possess multi-ligand binding properties.

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Organizational Affiliation: 

Key Laboratory for Protein Sciences of Ministry of Education, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clumping factor B	A	363	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0  Gene Names: clfB, SAR2709
Find proteins for Q6GDH2 (Staphylococcus aureus (strain MRSA252)) Explore Q6GDH2  Go to UniProtKB:  Q6GDH2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.289 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.423	α = 90
b = 94.423	β = 90
c = 86.717	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-07 
• Released Date: 2012-08-08 
Deposition Author(s): Yang, M.J., Xiang, H., Wang, J.W., Liu, B., Chen, Y.G., Liu, L., Deng, X.M., Feng, Y.

Revision History 

• Version 1.0: 2012-08-08
  Type: Initial release