PDBsum entry: 3g6j

Immune system

PDB id: 3g6j

Contents

Protein chains

642 a.a. *

903 a.a. *

214 a.a. *

221 a.a. *

Metals

_CA ×2

* Residue conservation analysis

PDB id:

3g6j

Name:

Immune system

Title:

C3b in complex with a c3b specific fab

Structure:

Complement c3 beta chain. Chain: a, c. Synonym: complement c3, c3 and pzp-like alpha-2-macroglobul containing protein 1. Complement c3 alpha chain. Chain: b, d. Synonym: complement c3, c3 and pzp-like alpha-2-macroglobul containing protein 1. Fab light chain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Resolution:

3.10Å R-factor: 0.218 R-free: 0.282

Authors:

C.Wiesmann

Key ref:

K.J.Katschke et al. (2009). Structural and Functional Analysis of a C3b-specific Antibody That Selectively Inhibits the Alternative Pathway of Complement. J Biol Chem, 284, 10473-10479. PubMed id: 19196712 DOI: 10.1074/jbc.M809106200

Date:

06-Feb-09 Release date: 10-Mar-09

Protein chains

P01024  (CO3_HUMAN) -  Complement C3

Seq: 1663 a.a.

Struc: 642 a.a.

Protein chains

P01024  (CO3_HUMAN) -  Complement C3

Seq: 1663 a.a.

Struc: 903 a.a.

Protein chain

No UniProt id for this chain

Protein chain

No UniProt id for this chain

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (2 terms)
• Biochemical function: protein binding (2 terms)

DOI no: 10.1074/jbc.M809106200

J Biol Chem 284:10473-10479 (2009)

PubMed id: 19196712

Structural and Functional Analysis of a C3b-specific Antibody That Selectively Inhibits the Alternative Pathway of Complement.

K.J.Katschke, S.Stawicki, J.Yin, M.Steffek, H.Xi, L.Sturgeon, P.E.Hass, K.M.Loyet, L.Deforge, Y.Wu, M.van Lookeren Campagne, C.Wiesmann.

ABSTRACT

Amplification of the complement cascade through the alternative pathway can lead to excessive inflammation. Targeting C3b, a component central to the alternative pathway of complement, provides a powerful approach to inhibit complement-mediated immune responses and tissue injury. In the present study, phage display technology was employed to generate an antibody that selectively recognizes C3b but not the non-activated molecule C3. The crystal structure of C3b in complex with a Fab fragment of this antibody (S77) illustrates the structural basis for this selectivity. Cleavage of C3 to C3b results in a plethora of structural changes within C3, including the rearrangement of macroglobulin domain 6 enabling binding of S77 to the adjacent macroglobulin domain 7 domain. S77 blocks binding of factor B to C3b inhibiting the first step in the formation of the alternative pathway C3 convertase. In addition, S77 inhibits C5 binding to C3b. This results in significantly reduced formations of anaphylatoxins and membrane-attack complexes. This study for the first time demonstrates the structural basis for complement inhibition by a C3b-selective antibody and provides insights into the molecular mechanisms of alternative pathway complement activation.

Selected figure(s)

Figure 2.
Crystal structure of S77 in complex with C3b. A, structure of the C3b-S77 dimer in the asymmetric unit. One C3b-S77 complex is shown as a ribbon diagram; the other is in surface representation. The β-chains of C3b are depicted in green, the α-chains shown in violet, light blue (TED domain), and orange (CUB domain). S77 is shown with the light chains colored white, and the heavy chains colored yellow. B, the Fab surface is shown with the light chain atoms in white and heavy chain in yellow. All amino acids that have at least one atom closer than 4.5 Å to the S77 are shown in stick representation and are labeled with carbon atoms of residues from the β-chain and α-chain colored green and violet, respectively. C, the S77 binding site of C3b. Atoms of C3b that are closer than 4.5, 4, and 3.5 Å are colored yellow, orange, and red, respectively. D, the surface of C3 is shown after superimposing the MG7 domain of C3 onto the MG7 domain of the C3b-S77 complex. Although the MG7 domains of C3 and C3b superimpose very well (r.m.s.d. 0.5 Å for 97 common Cα positions), the different relative orientation of MG7 in respect to MG6 leads to steric clashes between the light chain of the S77 and the MG6 domain in a potential complex, thus preventing S77 binding to C3.

Figure 7.
Structural basis for complement inhibition by S77, CRIg, and compstatin. The superposition of the C3b-S77 complex, the C3c-CRIg complex, and the C3c-compstatin complex shows that all three inhibitors recognize the same “face” of the complement protein; their binding sites are located on the opposite site of the TED position in C3b. C3b-C3c and S77 are colored as described in Fig. 2, CRIg is shown in red, and compstatin is depicted as purple sticks.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 10473-10479) copyright 2009.

Figures were selected by the author.