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


This is version 1.1 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: 10.1126/science.1195821
  • Structures With Same Primary Citation

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C3B BETA CHAIN
A, C
642Homo 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: 2
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C3B ALPHA' CHAIN
B, D
912Homo 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: 3
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT FACTOR B
F, H
732Homo sapiensMutation(s): 2 
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

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT FACTOR D
I, J
228Homo sapiensMutation(s): 1 
Gene Names: CFDDFPFD
EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens)
Go to UniProtKB:  P00746
NIH Common Fund Data Resources
PHAROS  P00746
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C, D, F, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
F, H
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-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