4D9Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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 alter ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Factor DAB228Macaca mulattaMutation(s): 0 
Gene Names: CFD
EC: 3.4.21.46
Find proteins for F6YBP7 (Macaca mulatta)
Explore F6YBP7 
Go to UniProtKB:  F6YBP7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Anti-Factor D, light chainDL213Homo sapiensMutation(s): 0 
Find proteins for Q8TCD0 (Homo sapiens)
Explore Q8TCD0 
Go to UniProtKB:  Q8TCD0
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Anti-Factor D, heavy chainEH217Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, D, E, H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, D, H, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.33α = 90
b = 80.76β = 107.19
c = 142.63γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
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: 2014-04-02
    Changes: Structure summary
  • Version 1.4: 2017-08-02
    Changes: Refinement description, Source and taxonomy