3G6J

C3b in complex with a C3b specific Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

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

(2009) J.Biol.Chem. 284: 10473-10479

  • DOI: 10.1074/jbc.M809106200

  • PubMed 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 immun ...

    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.


    Organizational Affiliation

    Departments of Immunology, Antibody Engineering, Protein Engineering, Assay & Automation Technology, and Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement C3 beta chain
A, C
644Homo sapiensMutation(s): 0 
Gene Names: C3 (CPAMD1)
Find proteins for P01024 (Homo sapiens)
Go to Gene View: C3
Go to UniProtKB:  P01024
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Complement C3 alpha chain
B, D
915Homo sapiensMutation(s): 0 
Gene Names: C3 (CPAMD1)
Find proteins for P01024 (Homo sapiens)
Go to Gene View: C3
Go to UniProtKB:  P01024
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab light chain
E, G
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab heavy chain
F, H
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 216.436α = 90.00
b = 180.417β = 115.73
c = 154.584γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-02-06 
  • Released Date: 2009-03-10 
  • Deposition Author(s): Wiesmann, C.

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance