Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.87 kDa 
• Atom Count: 5840 
• Modelled Residue Count: 727 
• Deposited Residue Count: 766 
• Unique protein chains: 1

5DUQ

Active human c1-inhibitor in complex with dextran sulfate

• PDB DOI: 10.2210/pdb5DUQ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2015-09-20 Released: 2016-08-31 
• Deposition Author(s): Dijk, M., Holkers, J., Voskamp, P., Giannetti, B.M., Waterreus, W.J., van Veen, H.A., Pannu, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.278 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

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

• PubMed: 27818099 
• DOI: 10.1016/j.str.2016.09.013
• Primary Citation of Related Structures:  
  5DU3, 5DUQ


• 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 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.

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Organizational Affiliation: 

Department of Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasma protease C1 inhibitor	A, B	383	Homo sapiens	Mutation(s): 0  Gene Names: SERPING1, C1IN, C1NH
UniProt & NIH Common Fund Data Resources
Find proteins for P05155 (Homo sapiens) Explore P05155  Go to UniProtKB:  P05155
PHAROS:  P05155

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G86802XL GlyCosmos:  G86802XL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLC	E [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
SO3	G [auth B]	SULFITE ION O3 S LSNNMFCWUKXFEE-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900023	C	alpha-cellobiose	Oligosaccharide / Metabolism		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.278 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.1	α = 90
b = 197.424	β = 103.31
c = 56.779	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-09-20 
• Released Date: 2016-08-31 
Deposition Author(s): Dijk, M., Holkers, J., Voskamp, P., Giannetti, B.M., Waterreus, W.J., van Veen, H.A., Pannu, N.S.

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary