PDBsum entry 1edk

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protein links
Immunoglobulin-binding protein PDB id
Jmol PyMol
Protein chain
56 a.a. *
* Residue conservation analysis
PDB id:
Name: Immunoglobulin-binding protein
Title: Staphylococcal protein a e-domain (-60), nmr, minimized average structure
Structure: Staphylococcal protein a. Chain: a. Fragment: e-domain. Engineered: yes. Other_details: phe 11 chi 1 rotomer is -60 degrees
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 1 models
Authors: M.A.Starovasnik,N.J.Skelton,W.J.Fairbrother
Key ref:
M.A.Starovasnik et al. (1996). Solution structure of the E-domain of staphylococcal protein A. Biochemistry, 35, 15558-15569. PubMed id: 8952510 DOI: 10.1021/bi961409x
22-Jul-96     Release date:   01-Apr-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P38507  (SPA_STAAU) -  Immunoglobulin G-binding protein A
508 a.a.
56 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     pathogenesis   1 term 
  Biochemical function     immunoglobulin binding     1 term  


DOI no: 10.1021/bi961409x Biochemistry 35:15558-15569 (1996)
PubMed id: 8952510  
Solution structure of the E-domain of staphylococcal protein A.
M.A.Starovasnik, N.J.Skelton, M.P.O'Connell, R.F.Kelley, D.Reilly, W.J.Fairbrother.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21047817 R.Day, K.P.Lennox, D.B.Dahl, M.Vannucci, and J.W.Tsai (2010).
Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure.
  Bioinformatics, 26, 3059-3066.  
20835432 T.Jin, D.K.Tiwari, S.Tanaka, Y.Inouye, K.Yoshizawa, and T.M.Watanabe (2010).
Antibody-ProteinA conjugated quantum dots for multiplexed imaging of surface receptors in living cells.
  Mol Biosyst, 6, 2325-2331.  
19995192 P.Speziale, G.Pietrocola, S.Rindi, M.Provenzano, G.Provenza, A.Di Poto, L.Visai, and C.R.Arciola (2009).
Structural and functional role of Staphylococcus aureus surface components recognizing adhesive matrix molecules of the host.
  Future Microbiol, 4, 1337-1352.  
17805951 H.S.Lee, J.Choi, and S.Yoon (2007).
QHELIX: a computational tool for the improved measurement of inter-helical angles in proteins.
  Protein J, 26, 556-561.  
16709567 M.I.Gómez, M.O'Seaghdha, M.Magargee, T.J.Foster, and A.S.Prince (2006).
Staphylococcus aureus protein A activates TNFR1 signaling through conserved IgG binding domains.
  J Biol Chem, 281, 20190-20196.  
14764606 D.R.Patel, H.J.Wallweber, J.Yin, S.K.Shriver, S.A.Marsters, N.C.Gordon, M.A.Starovasnik, and R.F.Kelley (2004).
Engineering an APRIL-specific B cell maturation antigen.
  J Biol Chem, 279, 16727-16735.  
14718654 D.Zheng, J.M.Aramini, and G.T.Montelione (2004).
Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.
  Protein Sci, 13, 549-554.
PDB code: 1q2n
15048831 M.Linhult, S.Gülich, T.Gräslund, A.Simon, M.Karlsson, A.Sjöberg, K.Nord, and S.Hober (2004).
Improving the tolerance of a protein a analogue to repeated alkaline exposures using a bypass mutagenesis approach.
  Proteins, 55, 407-416.  
12660242 G.González-Sapienza, and R.E.Cachau (2003).
Identification of critical residues of an immunodominant region of Echinococcus granulosus antigen B.
  J Biol Chem, 278, 20179-20184.  
11830661 G.R.Nakamura, M.E.Reynolds, Y.M.Chen, M.A.Starovasnik, and H.B.Lowman (2002).
Stable "zeta" peptides that act as potent antagonists of the high-affinity IgE receptor.
  Proc Natl Acad Sci U S A, 99, 1303-1308.
PDB codes: 1kcn 1kco
10805799 M.Graille, E.A.Stura, A.L.Corper, B.J.Sutton, M.J.Taussig, J.B.Charbonnier, and G.J.Silverman (2000).
Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity.
  Proc Natl Acad Sci U S A, 97, 5399-5404.
PDB code: 1dee
10532240 A.Karimi, M.Matsumura, P.E.Wright, and H.J.Dyson (1999).
Characterization of monomeric and dimeric B domain of Staphylococcal protein A.
  J Pept Res, 54, 344-352.  
  10422830 M.A.Starovasnik, M.P.O'Connell, W.J.Fairbrother, and R.F.Kelley (1999).
Antibody variable region binding by Staphylococcal protein A: thermodynamic analysis and location of the Fv binding site on E-domain.
  Protein Sci, 8, 1423-1431.  
9437429 J.Gitschier, B.Moffat, D.Reilly, W.I.Wood, and W.J.Fairbrother (1998).
Solution structure of the fourth metal-binding domain from the Menkes copper-transporting ATPase.
  Nat Struct Biol, 5, 47-54.
PDB codes: 1aw0 2aw0
9565750 J.P.Schneider, A.Lombardi, and W.F.DeGrado (1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
  Fold Des, 3, R29-R40.  
9294166 M.A.Starovasnik, A.C.Braisted, and J.A.Wells (1997).
Structural mimicry of a native protein by a minimized binding domain.
  Proc Natl Acad Sci U S A, 94, 10080-10085.
PDB codes: 1zda 1zdb 1zdc 1zdd
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.