3G6J

C3b in complex with a C3b specific Fab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 

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
  • Primary Citation of Related Structures:  
    3G6J

  • 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 immune re ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C3 beta chain A, C644Homo sapiensMutation(s): 0 
Gene Names: C3, CPAMD1
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS:  P01024
GTEx:  ENSG00000125730
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C3 alpha chain B, D915Homo sapiensMutation(s): 0 
Gene Names: C3, CPAMD1
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS:  P01024
GTEx:  ENSG00000125730
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab light chain E, G214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fab heavy chain F, H226Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 216.436α = 90
b = 180.417β = 115.73
c = 154.584γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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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
    Changes: Advisory, Refinement description, Version format compliance