4DTE

Crystal structure of zebrafish plasminogen activator inhibitor-1 (PAI-1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Protein conformational change delayed by steric hindrance from an N-linked glycan.

Bager, R.Johansen, J.S.Jensen, J.K.Stensballe, A.Jendroszek, A.Buxbom, L.Sorensen, H.P.Andreasen, P.A.

(2013) J.Mol.Biol. 425: 2867-2877

  • DOI: 10.1016/j.jmb.2013.05.007
  • Primary Citation of Related Structures:  4KDS

  • PubMed Abstract: 
  • Very few studies have attributed a direct, active, functional role to N-linked glycans. We describe here an N-linked glycan with a unique role for maintaining the active conformation of a protein of the serpin family. The distinguishing feature of se ...

    Very few studies have attributed a direct, active, functional role to N-linked glycans. We describe here an N-linked glycan with a unique role for maintaining the active conformation of a protein of the serpin family. The distinguishing feature of serpins is the "stressed-to-relaxed" transition, in which the reactive center loop inserts as a β-strand into the central β-sheet A. This transition forms the basis for the conversion of serpins to the inactive latent state. We demonstrate that plasminogen activator inhibitor-1 (PAI-1) from zebrafish converts to the latent state about 5-fold slower than human PAI-1. In contrast to human PAI-1, fish PAI-1 carries a single N-linked glycan at Asn185 in the gate region through which the reactive center loop passes during latency transition. While the latency transition of human PAI-1 is unaffected by deglycosylation, deglycosylated zebrafish PAI-1 (zfPAI-1) goes latent about 50-fold faster than the glycosylated zfPAI-1 and about 25-fold faster than non-glycosylated human PAI-1. X-ray crystal structure analysis of glycosylated fish PAI-1 confirmed the presence of an N-linked glycan in the gate region and a lack of glycan-induced structural changes. Thus, latency transition of zfPAI-1 is delayed by steric hindrance from the glycan in the gate region. Our findings reveal a previously unknown mechanism for inhibition of protein conformational changes by steric hindrance from N-linked glycans.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
A, B
374Danio rerioGene Names: serpine1
Find proteins for F1QRB8 (Danio rerio)
Go to UniProtKB:  F1QRB8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 1.96 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.160α = 90.00
b = 73.770β = 102.73
c = 91.750γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-02-21 
  • Released Date: 2013-03-27 
  • Deposition Author(s): Johansen, J.S.

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-10
    Type: Other
  • Version 1.2: 2013-08-07
    Type: Database references
  • Version 1.3: 2013-08-14
    Type: Database references
  • Version 1.4: 2013-08-21
    Type: Database references, Structure summary
  • Version 1.5: 2017-11-15
    Type: Refinement description