5DUQ

Active human c1-inhibitor in complex with dextran sulfate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

How Dextran Sulfate Affects C1-inhibitor Activity: A Model for Polysaccharide Potentiation.

Dijk, M., Holkers, J., Voskamp, P., Giannetti, B.M., Waterreus, W.J., van Veen, H.A., Pannu, N.S.

(2016) Structure 24: 2182-2189

  • DOI: 10.1016/j.str.2016.09.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • C1-inhibitor is a key inhibitor of the complement and contact activation systems, and mutations in the protein can cause hereditary angioedema. Through an unknown mechanism, polysaccharides can increase C1-inhibitor activity against some of its targe ...

    C1-inhibitor is a key inhibitor of the complement and contact activation systems, and mutations in the protein can cause hereditary angioedema. Through an unknown mechanism, polysaccharides can increase C1-inhibitor activity against some of its target proteases. Here we present the crystal structures of the serine protease inhibitor (serpin) domain of active C1-inhibitor by itself and in complex with dextran sulfate. Unlike previously described interactions of serpins with polysaccharides, the structures and isothermal titration calorimetry experiments together reveal that dextran sulfate binds to C1-inhibitor's F1 helix with low affinity and does not invoke an allosteric change. Furthermore, one dextran sulfate molecule can bind multiple C1-inhibitor molecules. We propose that in a C1-inhibitor/protease/polysaccharide ternary complex, negatively charged polysaccharides link C1-inhibitor's positively charged F1 helix to positively charged autolysis loops of proteases. The proposed mechanism elegantly explains previous experiments showing that polysaccharide potentiation is increased against proteases with a greater positive charge in their autolysis loop.

    Organizational Affiliation: 

    Department of Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasma protease C1 inhibitor
A, B
383Homo sapiensMutation(s): 0 
Gene Names: SERPING1 (C1IN, C1NH)
Find proteins for P05155 (Homo sapiens)
Go to Gene View: SERPING1
Go to UniProtKB:  P05155
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO3
Query on SO3
Download SDF File 
Download CCD File 
B
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
BGC
Query on BGC
Download SDF File 
Download CCD File 
B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GLC
Query on GLC
Download SDF File 
Download CCD File 
A, B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.100α = 90.00
b = 197.424β = 103.31
c = 56.779γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references