6RU3

Crystal structure of the FP specific nanobody hFPNb1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System.

Pedersen, D.V.Gadeberg, T.A.F.Thomas, C.Wang, Y.Joram, N.Jensen, R.K.Mazarakis, S.M.M.Revel, M.El Sissy, C.Petersen, S.V.Lindorff-Larsen, K.Thiel, S.Laursen, N.S.Fremeaux-Bacchi, V.Andersen, G.R.

(2019) Front Immunol 10: 2007-2007

  • DOI: https://doi.org/10.3389/fimmu.2019.02007
  • Primary Citation of Related Structures:  
    6RU3, 6RU5, 6RUR, 6RUS, 6RUV, 6RV6, 6SEJ

  • PubMed Abstract: 

    Properdin (FP) is a positive regulator of the immune system stimulating the activity of the proteolytically active C3 convertase C3bBb in the alternative pathway of the complement system. Here we present two crystal structures of FP and two structures of convertase bound FP. A structural core formed by three thrombospondin repeats (TSRs) and a TB domain harbors the convertase binding site in FP that mainly interacts with C3b. Stabilization of the interaction between the C3b C-terminus and the MIDAS bound Mg 2+ in the Bb protease by FP TSR5 is proposed to underlie FP convertase stabilization. Intermolecular contacts between FP and the convertase subunits suggested by the structure were confirmed by binding experiments. FP is shown to inhibit C3b degradation by FI due to a direct competition for a common binding site on C3b. FP oligomers are held together by two sets of intermolecular contacts, where the first is formed by the TB domain from one FP molecule and TSR4 from another. The second and largest interface is formed by TSR1 and TSR6 from the same two FP molecules. Flexibility at four hinges between thrombospondin repeats is suggested to enable the oligomeric, polydisperse, and extended architecture of FP. Our structures rationalize the effects of mutations associated with FP deficiencies and provide a structural basis for the analysis of FP function in convertases and its possible role in pattern recognition.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hFP1Nb1A [auth C]131Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.12α = 90
b = 65.12β = 90
c = 169.26γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR155-2015-2666

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Structure summary