4WWI

Crystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.307 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Suppression of conformational heterogeneity at a protein-protein interface.

Deis, L.N.Wu, Q.Wang, Y.Qi, Y.Daniels, K.G.Zhou, P.Oas, T.G.

(2015) Proc.Natl.Acad.Sci.USA 112: 9028-9033

  • DOI: 10.1073/pnas.1424724112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Staphylococcal protein A (SpA) is an important virulence factor from Staphylococcus aureus responsible for the bacterium's evasion of the host immune system. SpA includes five small three-helix-bundle domains that can each bind with high affinity to ...

    Staphylococcal protein A (SpA) is an important virulence factor from Staphylococcus aureus responsible for the bacterium's evasion of the host immune system. SpA includes five small three-helix-bundle domains that can each bind with high affinity to many host proteins such as antibodies. The interaction between a SpA domain and the Fc fragment of IgG was partially elucidated previously in the crystal structure 1FC2. Although informative, the previous structure was not properly folded and left many substantial questions unanswered, such as a detailed description of the tertiary structure of SpA domains in complex with Fc and the structural changes that take place upon binding. Here we report the 2.3-Å structure of a fully folded SpA domain in complex with Fc. Our structure indicates that there are extensive structural rearrangements necessary for binding Fc, including a general reduction in SpA conformational heterogeneity, freezing out of polyrotameric interfacial residues, and displacement of a SpA side chain by an Fc side chain in a molecular-recognition pocket. Such a loss of conformational heterogeneity upon formation of the protein-protein interface may occur when SpA binds its multiple binding partners. Suppression of conformational heterogeneity may be an important structural paradigm in functionally plastic proteins.


    Organizational Affiliation

    Department of Biochemistry, Duke University, Durham, NC 27710.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G-binding protein A
A, B, C
58Staphylococcus aureusMutation(s): 0 
Gene Names: spa
Find proteins for P38507 (Staphylococcus aureus)
Go to UniProtKB:  P38507
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ig gamma-3 chain C region
D, E, F
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.307 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 138.918α = 90.00
b = 88.116β = 90.95
c = 101.038γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-11-11 
  • Released Date: 2015-07-15 
  • Deposition Author(s): Deis, L.N., Oas, T.G.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM081666

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Derived calculations
  • Version 1.2: 2015-07-29
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Source and taxonomy