4D9R

Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Inhibiting alternative pathway complement activation by targeting the factor d exosite.

Katschke, K.J., Wu, P., Ganesan, R., Kelley, R.F., Mathieu, M.A., Hass, P.E., Murray, J., Kirchhofer, D., Wiesmann, C., van Lookeren Campagne, M.

(2012) J Biol Chem 287: 12886-12892

  • DOI: 10.1074/jbc.M112.345082
  • Primary Citation of Related Structures:  
    4D9Q, 4D9R

  • PubMed Abstract: 

    • By virtue of its amplifying property, the alternative complement pathway has been implicated in a number of inflammatory diseases and constitutes an attractive therapeutic target. An anti-factor D Fab fragment (AFD) was generated to inhibit the alternati ...

    By virtue of its amplifying property, the alternative complement pathway has been implicated in a number of inflammatory diseases and constitutes an attractive therapeutic target. An anti-factor D Fab fragment (AFD) was generated to inhibit the alternative complement pathway in advanced dry age-related macular degeneration. AFD potently prevented factor D (FD)-mediated proteolytic activation of its macromolecular substrate C3bB, but not proteolysis of a small synthetic substrate, indicating that AFD did not block access of the substrate to the catalytic site. The crystal structures of AFD in complex with human and cynomolgus FD (at 2.4 and 2.3 Å, respectively) revealed the molecular details of the inhibitory mechanism. The structures show that the AFD-binding site includes surface loops of FD that form part of the FD exosite. Thus, AFD inhibits FD proteolytic function by interfering with macromolecular substrate access rather than by inhibiting FD catalysis, providing the molecular basis of AFD-mediated inhibition of a rate-limiting step in the alternative complement pathway.

    Organizational Affiliation: 

    Department of Immunology, Genentech Incorporated, South San Francisco, California 94080, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement factor D A, B228Homo sapiensMutation(s): 0 
Gene Names: CFD, DF, Factor D, PFD
EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens)
Explore P00746 
Go to UniProtKB:  P00746
NIH Common Fund Data Resources
PHAROS:  P00746
GTEx:  ENSG00000197766
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab light chain D, L214Homo sapiensMutation(s): 0 
Gene Names: IGKC
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
NIH Common Fund Data Resources
PHAROS:  P01834
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab heavy chain E, H218Homo sapiensMutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
NIH Common Fund Data Resources
PHAROS:  P01857
GTEx:  ENSG00000211896
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download Ideal Coordinates CCD File 
D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FABKd :  0.004000000189989805   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.048α = 90
b = 132.048β = 90
c = 180.288γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-03-14
    Changes: Database references
  • Version 1.2: 2012-05-02
    Changes: Database references
  • Version 1.3: 2013-09-18
    Changes: Database references
  • Version 1.4: 2017-08-02
    Changes: Advisory, Refinement description, Source and taxonomy