Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83295.59 
• Atom Count: 5346 
• Residue Count: 767 
• Unique protein chains: 3

5JQ6

Crystal structure of ClfA in complex with the Fab fragment of Tefibazumab

• DOI: 10.2210/pdb5JQ6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Staphylococcus aureus (strain Newman)
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): 2 


• Deposited: 2016-05-04 Released: 2017-01-18 
• Deposition Author(s): Ganesh, V.K.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.259 
• R-Value Work: 0.208 

Literature

Lessons from the Crystal Structure of the S. aureus Surface Protein Clumping Factor A in Complex With Tefibazumab, an Inhibiting Monoclonal Antibody.

Ganesh, V.K., Liang, X., Geoghegan, J.A., Cohen, A.L., Venugopalan, N., Foster, T.J., Hook, M.

(2016) EBioMedicine 13: 328-338

• PubMed: 27789272 
• DOI: 10.1016/j.ebiom.2016.09.027


• PubMed Abstract: 
  

The Staphylococcus aureus fibrinogen binding MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules), ClfA (clumping factor A) is an important virulence factor in staphylococcal infections and a component of several vaccines currently under clinical evaluation. The mouse monoclonal antibody aurexis (also called 12-9), and the humanized version tefibazumab are therapeutic monoclonal antibodies targeting ClfA that in combination with conventional antibiotics were effective in animal models but showed less impressive efficacy in a limited Phase II clinical trial. We here report the crystal structure and a biochemical characterization of the ClfA/tefibazumab (Fab) complex. The epitope for tefibazumab is located to the "top" of the N3 subdomain of ClfA and partially overlaps with a previously unidentified second binding site for fibrinogen. A high-affinity binding of ClfA to fibrinogen involves both an interaction at the N3 site and the previously identified docking of the C-terminal segment of the fibrinogen γ-chain in the N2N3 trench. Although tefibazumab binds ClfA with high affinity we observe a modest IC50 value for the inhibition of fibrinogen binding to the MSCRAMM. This observation, paired with a common natural occurring variant of ClfA that is not effectively recognized by the mAb, may partly explain the modest effect tefibazumab showed in the initial clinic trail. This information will provide guidance for the design of the next generation of therapeutic anti-staphylococcal mAbs targeting ClfA.

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Organizational Affiliation: 

Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A & M University Health Science Center, 2121 W Holcombe Blvd., Houston, TX 77030, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Clumping factor A	A	329	Staphylococcus aureus (strain Newman)	Mutation(s): 2  Gene Names: clfA
Find proteins for Q53653 (Staphylococcus aureus (strain Newman)) Go to UniProtKB:  Q53653

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Tefibazumab FAB FRAGMENT HEAVY CHAIN	H	222	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Tefibazumab FAB FRAGMENT LIGHT CHAIN	L	216	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.259 
• R-Value Work: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 234.287	α = 90.00
b = 84.086	β = 98.90
c = 48.626	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-05-04 
• Released Date: 2017-01-18 
• Deposition Author(s): Ganesh, V.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	R01AI20624

Revision History 

• Version 1.0: 2017-01-18
  Type: Initial release
• Version 1.1: 2017-09-13
  Type: Author supporting evidence