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 

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This is version 2.1 of the entry. See complete history


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

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT C3B BETA CHAIN
A, C
642Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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Go to UniProtKB:  P01024
GTEx:  ENSG00000125730 
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UniProt GroupP01024
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT C3B ALPHA' CHAIN
B, D
912Homo sapiensMutation(s): 0 
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Go to UniProtKB:  P01024
GTEx:  ENSG00000125730 
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UniProt GroupP01024
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT FACTOR BE [auth F],
F [auth H]
732Homo sapiensMutation(s): 2 
EC: 3.4.21.47
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Find proteins for P00751 (Homo sapiens)
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GTEx:  ENSG00000243649 
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UniProt GroupP00751
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT FACTOR DG [auth I],
H [auth J]
228Homo sapiensMutation(s): 1 
EC: 3.4.21.46
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Find proteins for P00746 (Homo sapiens)
Explore P00746 
Go to UniProtKB:  P00746
GTEx:  ENSG00000197766 
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Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth E],
J [auth G],
K
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains 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
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
P [auth D],
R [auth F],
S [auth F],
U [auth H],
V [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

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W [auth I],
X [auth J]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth A],
O [auth C],
Q [auth F],
T [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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  (Full details and data files)

  • 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
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary