2WIN

C3 convertase (C3bBb) stabilized by SCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and functional implications of the alternative complement pathway C3 convertase stabilized by a staphylococcal inhibitor.

Rooijakkers, S.H.Wu, J.Ruyken, M.van Domselaar, R.Planken, K.L.Tzekou, A.Ricklin, D.Lambris, J.D.Janssen, B.J.van Strijp, J.A.Gros, P.

(2009) Nat. Immunol. 10: 721-727

  • DOI: 10.1038/ni.1756

  • PubMed Abstract: 
  • Activation of the complement system generates potent chemoattractants and leads to the opsonization of cells for immune clearance. Short-lived protease complexes cleave complement component C3 into anaphylatoxin C3a and opsonin C3b. Here we report th ...

    Activation of the complement system generates potent chemoattractants and leads to the opsonization of cells for immune clearance. Short-lived protease complexes cleave complement component C3 into anaphylatoxin C3a and opsonin C3b. Here we report the crystal structure of the C3 convertase formed by C3b and the protease fragment Bb, which was stabilized by the bacterial immune-evasion protein SCIN. The data suggest that the proteolytic specificity and activity depend on the formation of dimers of C3 with C3b of the convertase. SCIN blocked the formation of a productive enzyme-substrate complex. Irreversible dissociation of the complex of C3b and Bb is crucial to complement regulation and was determined by slow binding kinetics of the Mg(2+)-adhesion site in Bb. Understanding the mechanistic basis of the central complement-activation step and microbial immune evasion strategies targeting this step will aid in the development of complement therapeutics.


    Organizational Affiliation

    Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C3 BETA CHAIN
A, C, E, G
645Homo sapiensGene Names: C3 (CPAMD1)
Find proteins for P01024 (Homo sapiens)
Go to Gene View: C3
Go to UniProtKB:  P01024
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C3B ALPHA' CHAIN
B, D, F, H
915Homo sapiensGene 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
I, J, K, L
507Homo sapiensGene 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
M, N, P, Q
92Staphylococcus aureus (strain MRSA252)Gene Names: scn
Find proteins for Q6GFB4 (Staphylococcus aureus (strain MRSA252))
Go to UniProtKB:  Q6GFB4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

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

Download SDF File 
Download CCD File 
I, J, K, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 228.632α = 90.00
b = 121.491β = 91.64
c = 280.783γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Advisory, Database references, Source and taxonomy