2XWB

Crystal Structure of Complement C3b in complex with Factors B and D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report



Literature

Structures of C3B in Complex with Factors B and D Give Insight Into Complement Convertase Formation.

Forneris, F.Ricklin, D.Wu, J.Tzekou, A.Wallace, R.S.Lambris, J.D.Gros, P.

(2010) Science 330: 1816

  • DOI: 10.1126/science.1195821
  • Primary Citation of Related Structures:  
    2XWJ, 2XWA, 2XWB, 2XW9

  • PubMed Abstract: 
  • Activation of the complement cascade induces inflammatory responses and marks cells for immune clearance. In the central complement-amplification step, a complex consisting of surface-bound C3b and factor B is cleaved by factor D to generate active c ...

    Activation of the complement cascade induces inflammatory responses and marks cells for immune clearance. In the central complement-amplification step, a complex consisting of surface-bound C3b and factor B is cleaved by factor D to generate active convertases on targeted surfaces. We present crystal structures of the pro-convertase C3bB at 4 angstrom resolution and its complex with factor D at 3.5 angstrom resolution. Our data show how factor B binding to C3b forms an open "activation" state of C3bB. Factor D specifically binds the open conformation of factor B through a site distant from the catalytic center and is activated by the substrate, which displaces factor D's self-inhibitory loop. This concerted proteolytic mechanism, which is cofactor-dependent and substrate-induced, restricts complement amplification to C3b-tagged target cells.


    Organizational Affiliation

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COMPLEMENT C3B BETA CHAINAC642Homo 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' CHAINBD912Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
Find proteins for P01024 (Homo sapiens)
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PHAROS  P01024
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COMPLEMENT FACTOR BFH732Homo sapiensMutation(s): 2 
Gene Names: CFBBFBFD
EC: 3.4.21.47
Find proteins for P00751 (Homo sapiens)
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PHAROS  P00751
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
COMPLEMENT FACTOR DIJ228Homo sapiensMutation(s): 1 
Gene Names: CFDDFPFD
EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens)
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PHAROS  P00746
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, K
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
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
L, M
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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D, F, H
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
I, J
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, C, F, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.275α = 95.47
b = 135.775β = 110.69
c = 149.975γ = 113.39
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2012-04-11
    Changes: Database references, Non-polymer description, Other, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary