5M6W

Properdin in complex with alternative pathway C3 convertase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.289 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Functional and structural insight into properdin control of complement alternative pathway amplification.

Pedersen, D.V.Roumenina, L.Jensen, R.K.Gadeberg, T.A.Marinozzi, C.Picard, C.Rybkine, T.Thiel, S.Srensen, U.B.Stover, C.Fremeaux-Bacchi, V.Andersen, G.R.

(2017) EMBO J. 36: 1084-1099

  • DOI: 10.15252/embj.201696173

  • PubMed Abstract: 
  • Properdin (FP) is an essential positive regulator of the complement alternative pathway (AP) providing stabilization of the C3 and C5 convertases, but its oligomeric nature challenges structural analysis. We describe here a novel FP deficiency (E244K ...

    Properdin (FP) is an essential positive regulator of the complement alternative pathway (AP) providing stabilization of the C3 and C5 convertases, but its oligomeric nature challenges structural analysis. We describe here a novel FP deficiency (E244K) caused by a single point mutation which results in a very low level of AP activity. Recombinant FP E244K is monomeric, fails to support bacteriolysis, and binds weakly to C3 products. We compare this to a monomeric unit excised from oligomeric FP, which is also dysfunctional in bacteriolysis but binds the AP proconvertase, C3 convertase, C3 products and partially stabilizes the convertase. The crystal structure of such a FP-convertase complex suggests that the major contact between FP and the AP convertase is mediated by a single FP thrombospondin repeat and a small region in C3b. Small angle X-ray scattering indicates that FP E244K is trapped in a compact conformation preventing its oligomerization. Our studies demonstrate an essential role of FP oligomerization in vivo while our monomers enable detailed structural insight paving the way for novel modulators of complement.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Center for Structural Biology, Aarhus University, Aarhus, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement C3
A, G
645Homo 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
B, H
913Homo 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
Complement factor B
J, L
505Homo sapiensMutation(s): 0 
Gene Names: CFB (BF, BFD)
EC: 3.4.21.47
Find proteins for P00751 (Homo sapiens)
Go to Gene View: CFB
Go to UniProtKB:  P00751
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Staphylococcal complement inhibitor
N, Q
86Staphylococcus aureus (strain MRSA252)Mutation(s): 0 
Gene Names: scn
Find proteins for Q6GFB4 (Staphylococcus aureus (strain MRSA252))
Go to UniProtKB:  Q6GFB4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, G, H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, G, H, J, L
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, G, H, J, L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.289 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 634.870α = 90.00
b = 121.980β = 112.91
c = 264.420γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Lundbeck FoundationDenmarkBRAINSTRUC
Novo Nordisk FoundationDenmarkHallas Moeller Fellowship
Danish Council for Independent ResearchDenmarkCouncil for Nature and Universe

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2017-04-26
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Data collection