6RUV

Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the non-inhibitory nanobody hFPNb1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.15 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Structures With Same Primary Citation

  • 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 structure ...

    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 --: --

    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
Nanobody hFPNb1
R, S
131Lama glamaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Properdin
U, X
170Homo sapiensMutation(s): 0 
Gene Names: CFPPFC
Find proteins for P27918 (Homo sapiens)
Go to UniProtKB:  P27918
NIH Common Fund Data Resources
PHAROS  P27918

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Properdin
V, Y
221Homo sapiensMutation(s): 0 
Gene Names: CFPPFC
Find proteins for P27918 (Homo sapiens)
Go to UniProtKB:  P27918
NIH Common Fund Data Resources
PHAROS  P27918

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Complement C3
A, G
645Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
Find proteins for P01024 (Homo sapiens)
Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS  P01024

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Complement C3
B, H
915Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
Find proteins for P01024 (Homo sapiens)
Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS  P01024

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Complement factor B
J, L
505Homo sapiensMutation(s): 0 
Gene Names: CFBBFBFD
EC: 3.4.21.47
Find proteins for P00751 (Homo sapiens)
Go to UniProtKB:  P00751
NIH Common Fund Data Resources
PHAROS  P00751

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Inhibitor
N, Q
86Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for A0A0H2DUF0 (Staphylococcus aureus)
Go to UniProtKB:  A0A0H2DUF0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, G, H, J, L, V, Y
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
U, V, X, Y
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BGC
Query on BGC

Download CCD File 
U, V, X, Y
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

Download CCD File 
U, V, X, Y
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
J, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.15 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.99α = 90
b = 354.03β = 90
c = 367.84γ = 90
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 

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