3HS0

Cobra Venom Factor (CVF) in complex with human factor B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into complement convertase formation based on the structure of the factor B-cobra venom factor complex

Janssen, B.J.Gomes, L.Koning, R.I.Svergun, D.I.Koster, A.J.Fritzinger, D.C.Vogel, C.W.Gros, P.

(2009) Embo J. 28: 2469-2478

  • DOI: 10.1038/emboj.2009.184
  • Primary Citation of Related Structures:  3HRZ

  • PubMed Abstract: 
  • Immune protection by the complement system critically depends on assembly of C3 convertases on the surface of pathogens and altered host cells. These short-lived protease complexes are formed through pro-convertases, which for the alternative pathway ...

    Immune protection by the complement system critically depends on assembly of C3 convertases on the surface of pathogens and altered host cells. These short-lived protease complexes are formed through pro-convertases, which for the alternative pathway consist of the complement component C3b and the pro-enzyme factor B (FB). Here, we present the crystal structure at 2.2-A resolution, small-angle X-ray scattering and electron microscopy (EM) data of the pro-convertase formed by human FB and cobra venom factor (CVF), a potent homologue of C3b that generates more stable convertases. FB is loaded onto CVF through its pro-peptide Ba segment by specific contacts, which explain the specificity for the homologous C3b over the native C3 and inactive products iC3b and C3c. The protease segment Bb binds the carboxy terminus of CVF through the metal-ion dependent adhesion site of the Von Willebrand factor A-type domain. A possible dynamic equilibrium between a 'loading' and 'activation' state of the pro-convertase may explain the observed difference between the crystal structure of CVFB and the EM structure of C3bB. These insights into formation of convertases provide a basis for further development of complement therapeutics.


    Organizational Affiliation

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cobra venom factor
A, F
627Naja kaouthiaN/A
Find proteins for Q91132 (Naja kaouthia)
Go to UniProtKB:  Q91132
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cobra venom factor
B, G
252Naja kaouthiaN/A
Find proteins for Q91132 (Naja kaouthia)
Go to UniProtKB:  Q91132
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cobra venom factor
C, H
379Naja kaouthiaN/A
Find proteins for Q91132 (Naja kaouthia)
Go to UniProtKB:  Q91132
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Complement factor B
D, I
741Homo 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, D, F, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 134.026α = 90.00
b = 136.975β = 90.00
c = 283.740γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DNAdata collection
SCALAdata scaling
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance