2WIN

C3 convertase (C3bBb) stabilized by SCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    2WIN

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COMPLEMENT C3 BETA CHAINACEG645Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
Find proteins for P01024 (Homo sapiens)
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Go to UniProtKB:  P01024
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PHAROS  P01024
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COMPLEMENT C3B ALPHA' CHAINBDFH915Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
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PHAROS  P01024
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COMPLEMENT FACTOR BIJKL507Homo sapiensMutation(s): 0 
Gene Names: CFBBFBFD
EC: 3.4.21.47
Find proteins for P00751 (Homo sapiens)
Explore P00751 
Go to UniProtKB:  P00751
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PHAROS  P00751
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
STAPHYLOCOCCAL COMPLEMENT INHIBITORMNPQ92Staphylococcus aureusMutation(s): 0 
Find proteins for Q6GFB4 (Staphylococcus aureus (strain MRSA252))
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Go to UniProtKB:  Q6GFB4
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O, R, T, U
4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
S, W
5 N-Glycosylation Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
V
6 N-Glycosylation Oligosaccharides Interaction
Entity ID: 8
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
X
4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 9
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Y, a
3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 10
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Z
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 11
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
b
5 N-Glycosylation Oligosaccharides Interaction
Entity ID: 12
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
c
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
K, L
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

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B, K
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

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G
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
MG
Query on MG

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I, J, K, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.632α = 90
b = 121.491β = 91.64
c = 280.783γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Advisory, Database references, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary