Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Factor B structure provides insights into activation of the central protease of the complement system


Factor B is the central protease of the complement system of immune defense. Here, we present the crystal structure of human factor B at 2.3-Å resolution, which reveals how the five-domain proenzyme is kept securely inactive. The canonical activation helix of the Von Willebrand factor A (VWA) domain is displaced by a helix from the preceding domain linker. The two helices conformationally link the scissile-activation peptide and the metal ion–dependent adhesion site required for binding of the ligand C3b. The data suggest that C3b binding displaces the three N-terminal control domains and reshuffles the two central helices. Reshuffling of the helices releases the scissile bond for final proteolytic activation and generates a new interface between the VWA domain and the serine protease domain. This allosteric mechanism is crucial for tight regulation of the complement-amplification step in the immune response.

Your institute does not have access to this article

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: C3 convertase formation and crystal structure of complement factor B.
Figure 2: Regulatory elements in the VWA domain.
Figure 3: Domain orientations in factor B and Bb.

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank


  1. Carroll, M.C. The complement system in regulation of adaptive immunity. Nat. Immunol. 5, 981–986 (2004).

    CAS  Article  Google Scholar 

  2. Walport, M.J. Complement. First of two parts. N. Engl. J. Med. 344, 1058–1066 (2001).

    CAS  Article  Google Scholar 

  3. Fishelson, Z., Pangburn, M.K. & Muller-Eberhard, H.J. Characterization of the initial C3 convertase of the alternative pathway of human complement. J. Immunol. 132, 1430–1434 (1984).

    CAS  PubMed  Google Scholar 

  4. Xu, Y., Narayana, S.V. & Volanakis, J.E. Structural biology of the alternative pathway convertase. Immunol. Rev. 180, 123–135 (2001).

    CAS  Article  Google Scholar 

  5. Pangburn, M.K. & Muller-Eberhard, H.J. The C3 convertase of the alternative pathway of human complement. Enzymic properties of the bimolecular proteinase. Biochem. J. 235, 723–730 (1986).

    CAS  Article  Google Scholar 

  6. Pryzdial, E.L. & Isenman, D.E. Alternative complement pathway activation fragment Ba binds to C3b. Evidence that formation of the factor B-C3b complex involves two discrete points of contact. J. Biol. Chem. 262, 1519–1525 (1987).

    CAS  PubMed  Google Scholar 

  7. Horiuchi, T., Macon, K.J., Engler, J.A. & Volanakis, J.E. Site-directed mutagenesis of the region around Cys-241 of complement component C2. Evidence for a C4b binding site. J. Immunol. 147, 584–589 (1991).

    CAS  PubMed  Google Scholar 

  8. Emsley, J., Knight, C.G., Farndale, R.W., Barnes, M.J. & Liddington, R.C. Structural basis of collagen recognition by integrin alpha2beta1. Cell 101, 47–56 (2000).

    CAS  Article  Google Scholar 

  9. Springer, T.A. Complement and the multifaceted functions of VWA and integrin I domains. Structure 14, 1611–1616 (2006).

    CAS  Article  Google Scholar 

  10. Ponnuraj, K. et al. Structural analysis of engineered Bb fragment of complement factor B: insights into the activation mechanism of the alternative pathway C3-convertase. Mol. Cell 14, 17–28 (2004).

    CAS  Article  Google Scholar 

  11. Milder, F.J. et al. Structure of complement component C2a: implications for convertase formation and substrate binding. Structure 14, 1587–1597 (2006).

    CAS  Article  Google Scholar 

  12. Smith, C.A., Vogel, C.W. & Muller-Eberhard, H.J. MHC Class III products: an electron microscopic study of the C3 convertases of human complement. J. Exp. Med. 159, 324–329 (1984).

    CAS  Article  Google Scholar 

  13. Shimaoka, M. et al. Structures of the alpha L I domain and its complex with ICAM-1 reveal a shape-shifting pathway for integrin regulation. Cell 112, 99–111 (2003).

    CAS  Article  Google Scholar 

  14. Bhattacharya, A.A., Lupher, M.L., Jr., Staunton, D.E. & Liddington, R.C. Crystal structure of the A domain from complement factor B reveals an integrin-like open conformation. Structure 12, 371–378 (2004).

    CAS  Article  Google Scholar 

  15. Emsley, J., King, S.L., Bergelson, J.M. & Liddington, R.C. Crystal structure of the I domain from integrin alpha2beta1. J. Biol. Chem. 272, 28512–28517 (1997).

    CAS  Article  Google Scholar 

  16. Fishelson, Z., Pangburn, M.K. & Muller-Eberhard, H.J. C3 convertase of the alternative complement pathway. Demonstration of an active, stable C3b, Bb (Ni) complex. J. Biol. Chem. 258, 7411–7415 (1983).

    CAS  PubMed  Google Scholar 

  17. Hourcade, D.E., Mitchell, L., Kuttner-Kondo, L.A., Atkinson, J.P. & Medof, M.E. Decay-accelerating factor (DAF), complement receptor 1 (CR1), and factor H dissociate the complement AP C3 convertase (C3bBb) via sites on the type A domain of Bb. J. Biol. Chem. 277, 1107–1112 (2002).

    CAS  Article  Google Scholar 

  18. Hourcade, D.E., Mitchell, L.M. & Oglesby, T.J. Mutations of the type A domain of complement factor B that promote high-affinity C3b-binding. J. Immunol. 162, 2906–2911 (1999).

    CAS  PubMed  Google Scholar 

  19. Williams, S.C., Hinshelwood, J., Perkins, S.J. & Sim, R.B. Production and functional activity of a recombinant von Willebrand factor-A domain from human complement factor B. Biochem. J. 342, 625–632 (1999).

    CAS  Article  Google Scholar 

  20. Kam, C.M. et al. Human complement proteins D, C2, and B. Active site mapping with peptide thioester substrates. J. Biol. Chem. 262, 3444–3451 (1987).

    CAS  PubMed  Google Scholar 

  21. Khan, A.R. & James, M.N. Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes. Protein Sci. 7, 815–836 (1998).

    CAS  Article  Google Scholar 

  22. Hourcade, D.E., Wagner, L.M. & Oglesby, T.J. Analysis of the short consensus repeats of human complement factor B by site-directed mutagenesis. J. Biol. Chem. 270, 19716–19722 (1995).

    CAS  Article  Google Scholar 

  23. Xu, Y. & Volanakis, J.E. Contribution of the complement control protein modules of C2 in C4b binding assessed by analysis of C2/factor B chimeras. J. Immunol. 158, 5958–5965 (1997).

    CAS  PubMed  Google Scholar 

  24. Thurman, J.M. et al. A novel inhibitor of the alternative complement pathway prevents antiphospholipid antibody-induced pregnancy loss in mice. Mol. Immunol. 42, 87–97 (2005).

    CAS  Article  Google Scholar 

  25. Reeves, P.J., Callewaert, N., Contreras, R. & Khorana, H.G. Structure and function in rhodopsin: high-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N-acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line. Proc. Natl. Acad. Sci. USA 99, 13419–13424 (2002).

    CAS  Article  Google Scholar 

  26. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).

  27. Storoni, L.C., McCoy, A.J. & Read, R.J. Likelihood-enhanced fast rotation functions. Acta Crystallogr. D Biol. Crystallogr. 60, 432–438 (2004).

    Article  Google Scholar 

  28. Jing, H. et al. New structural motifs on the chymotrypsin fold and their potential roles in complement factor B. EMBO J. 19, 164–173 (2000).

    CAS  Article  Google Scholar 

  29. Perrakis, A., Morris, R. & Lamzin, V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458–463 (1999).

    CAS  Article  Google Scholar 

  30. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  Google Scholar 

  31. Terwilliger, T.C. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr. D Biol. Crystallogr. 59, 38–44 (2003).

    Article  Google Scholar 

  32. Winn, M.D., Isupov, M.N. & Murshudov, G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr. 57, 122–133 (2001).

    CAS  Article  Google Scholar 

  33. Janssen, B.J., Christodoulidou, A., McCarthy, A., Lambris, J.D. & Gros, P. Structure of C3b reveals conformational changes that underlie complement activity. Nature 444, 213–216 (2006).

    CAS  Article  Google Scholar 

  34. Wiesmann, C. et al. Structure of C3b in complex with CRIg gives insights into regulation of complement activation. Nature 444, 217–220 (2006).

    CAS  Article  Google Scholar 

Download references


We thank the European Synchrotron Radiation Facility for providing synchrotron radiation facilities and the beamline scientists at ID-14-EH4 for their help with data collection. This work was supported by a 'Pionier' program grant (P.G.) of the Council for Chemical Sciences of the Netherlands Organization for Scientific Research (NWO-CW).

Author information

Authors and Affiliations


Corresponding author

Correspondence to Piet Gros.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Stereo figure showing electron density (PDF 695 kb)

Supplementary Fig. 2

Activation state of the VWA domain (PDF 299 kb)

Supplementary Fig. 3

The serine protease domain catalytic center (PDF 177 kb)

Supplementary Fig. 4

The CCP triad arrangementF (PDF 400 kb)

Supplementary Fig. 5

The Mg2+-dependent C3b-binding site (PDF 366 kb)

Supplementary Table 1

Analysis of CCP domains 1–3 (PDF 37 kb)

Supplementary Table 2

Contacts between domains CCP1–CCP3 and the VWA and SP domains (PDF 43 kb)

Supplementary Methods (PDF 56 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Milder, F., Gomes, L., Schouten, A. et al. Factor B structure provides insights into activation of the central protease of the complement system. Nat Struct Mol Biol 14, 224–228 (2007).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing