3DY0

Crystal Structure of Cleaved PCI Bound to Heparin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The heparin binding site of protein C inhibitor is protease-dependent.

Li, W.Huntington, J.A.

(2008) J.Biol.Chem. 283: 36039-36045

  • DOI: 10.1074/jbc.M805974200

  • PubMed Abstract: 
  • Protein C inhibitor (PCI) is a member of the serpin family of protease inhibitors with many biological functions and broad inhibitory specificity. Its major targets in blood are thrombin and activated protein C (APC), and the inhibition of both enzym ...

    Protein C inhibitor (PCI) is a member of the serpin family of protease inhibitors with many biological functions and broad inhibitory specificity. Its major targets in blood are thrombin and activated protein C (APC), and the inhibition of both enzymes can be accelerated by glycosaminoglycans, including heparin. Acceleration of thrombin and APC inhibition by PCI requires that both protease and inhibitor bind to the same heparin chain to form a bridged Michaelis complex. However, the position of the heparin binding site of APC is opposite to that of thrombin, and formation of the bridged complexes must require either radical reorientation of the proteases relative to PCI or alternate heparin binding modes for PCI. In this study, we investigate how heparin bridges thrombin and APC to PCI by determining the effect of mutations in and around the putative heparin binding site of PCI. We found that heparin binds PCI in a linear fashion along helix H to bridge thrombin, consistent with our recent crystal structure (3B9F), but that it must rotate by approximately 60 degrees to engage Arg-229 to bridge APC. To gain insight into the possible modes of heparin binding to PCI, we solved a crystal structure of cleaved PCI bound to an octasaccharide heparin fragment to 1.55 angstroms resolution. The structure reveals a binding mode across the N terminus of helix H to engage Arg-229 and align the heparin binding site of APC. A molecular model for the heparin-bridged PCI.APC complex was built based on mutagenesis and structural data.


    Organizational Affiliation

    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-terminus Plasma serine protease inhibitor
A
336Homo sapiensMutation(s): 0 
Gene Names: SERPINA5 (PCI, PLANH3, PROCI)
Find proteins for P05154 (Homo sapiens)
Go to Gene View: SERPINA5
Go to UniProtKB:  P05154
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-terminus Plasma serine protease inhibitor
B
29Homo sapiensMutation(s): 0 
Gene Names: SERPINA5 (PCI, PLANH3, PROCI)
Find proteins for P05154 (Homo sapiens)
Go to Gene View: SERPINA5
Go to UniProtKB:  P05154
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SGN
Query on SGN

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Download CCD File 
A
N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
 Ligand Interaction
NO3
Query on NO3

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Download CCD File 
A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
IDS
Query on IDS

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Download CCD File 
A
2-O-sulfo-alpha-L-idopyranuronic acid
O2-SULFO-GLUCURONIC ACID
C6 H10 O10 S
COJBCAMFZDFGFK-VCSGLWQLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.051α = 90.00
b = 49.451β = 113.08
c = 64.969γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance