Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Solution structure of the E-domain of staphylococcal protein A.

Starovasnik, M.A.Skelton, N.J.O'Connell, M.P.Kelley, R.F.Reilly, D.Fairbrother, W.J.

(1996) Biochemistry 35: 15558-15569

  • DOI: https://doi.org/10.1021/bi961409x
  • Primary Citation of Related Structures:  
    1EDI, 1EDJ, 1EDK, 1EDL

  • PubMed Abstract: 

    The E-domain of staphylococcal protein A is one of five homologous IgG-binding domains designated E, D, A, B, and C that comprise the extracellular portion of protein A. The E-domain binds tightly to Fc fragments of IgG and binds certain Fv fragments with micromolar affinity. To explore further the structural features of Fc binding by protein A, and as a first step in developing a structural understanding of E-domain/Fv complex formation, we have determined the solution structure of the uncomplexed E-domain using 2D homonuclear and heteronuclear NMR spectroscopy. Complete 1H and 15N resonance assignments were obtained, and the structure was determined from 383 NOE-derived distance restrains, 34 phi and 19 chi 1 dihedral angle restraints, and 54 restraints for 27 H-bonds. 3JH alpha-H beta coupling constants and long-range NOEs involving Phe11 indicate the side chain exists in more than one conformation with differing chi 1 values. NOE restraints that were incompatible with chi 1 = -60 degrees were removed from one set of structure calculations, and those incompatible with chi 1 = 180 degrees were removed from a second set to allow Phe11 to explore both rotamer wells. Thus, two sets of 20 final structures, having no distance or dihedral angle restraint violations greater than 0.12 A or 1.6 degrees, respectively, represent the solution structure of the E-domain. Backbone atomic rms differences with respect to the mean coordinates for each set of 20 structures for residues 8-53 averaged 0.41 +/- 0.06 and 0.35 +/- 0.06 A. No significant differences in the overall structure result from the different orientations of Phe11. The solution structure of the E-domain consists of three alpha-helices that pack together to form a compact helical bundle. A detailed comparison between the E-domain ensembles and the previously determined structure for the B-domain in complex with Fc indicates that only the 180 degrees chi 1 rotamer of Phe11 is competent for binding; the -60 degrees chi 1 rotamer must reorient to 180 degrees to create a cavity that is filled by Ile253 from the CH2 domain of Fc in the Fc-bound complex.

  • Organizational Affiliation

    Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STAPHYLOCOCCAL PROTEIN A56Staphylococcus aureusMutation(s): 0 
Find proteins for P38507 (Staphylococcus aureus)
Explore P38507 
Go to UniProtKB:  P38507
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38507
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-05-22
    Changes: Data collection