6RUR

Structure of the SCIN stabilized C3bBb convertase bound to properdin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: 10.3389/fimmu.2019.02007
  • Primary Citation of Related Structures:  
    6SEJ, 6RU3, 6RU5, 6RUR, 6RUS, 6RUV, 6RV6

  • 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 ...

    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.


    Related Citations: 
    • Crystal structure of peptide-bound neprilysin reveals key binding interactions.
      Moss, S., Subramanian, V., Acharya, K.R.
      (2019) FEBS Lett --: --
    • Crystallization and X-ray analysis of monodisperse human properdin.
      Pedersen, D.V., Revel, M., Gadeberg, T.A.F., Andersen, G.R.
      (2019) Acta Crystallogr F Struct Biol Commun 75: 0

    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProperdinA [auth U], C [auth X]234Homo sapiensMutation(s): 0 
Gene Names: CFPPFC
Find proteins for P27918 (Homo sapiens)
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PHAROS:  P27918
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ProperdinB [auth V], D [auth Y]215Homo sapiensMutation(s): 0 
Gene Names: CFPPFC
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PHAROS:  P27918
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C3E [auth A], G645Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
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PHAROS:  P01024
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C3F [auth B], H915Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
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PHAROS:  P01024
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Complement factor BI [auth J], J [auth L]505Homo sapiensMutation(s): 0 
Gene Names: CFBBFBFD
EC: 3.4.21.47
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PHAROS:  P00751
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
InhibitorK [auth N], L [auth Q]85Staphylococcus aureusMutation(s): 0 
Gene Names: 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranoseM [auth C], N [auth D], P [auth F], Q [auth I]2 O-Glycosylation Oligosaccharides Interaction
Entity ID: 8
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseO [auth E], R [auth K]3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 9
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseS [auth M], T [auth O], U [auth P], V [auth R], W [auth S], X [auth T], Y [auth W], Z2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download Ideal Coordinates CCD File 
AA [auth U] , BA [auth U] , CA [auth V] , DA [auth V] , EA [auth V] , FA [auth V] , GA [auth V] , HA [auth V] , 
AA [auth U],  BA [auth U],  CA [auth V],  DA [auth V],  EA [auth V],  FA [auth V],  GA [auth V],  HA [auth V],  IA [auth V],  JA [auth X],  KA [auth X],  LA [auth Y],  MA [auth Y],  NA [auth Y],  OA [auth Y],  PA [auth Y],  QA [auth Y],  RA [auth Y]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
SA [auth B], TA [auth H]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 634.87α = 90
b = 121.98β = 112.91
c = 264.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary