4KDS | pdb_00004kds

Crystal structure of latent rainbow trout plasminogen activator inhibitor 1 (PAI-1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 
    0.218 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4KDS

This is version 1.3 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 Biology 425: 2867-2877

  • DOI: https://doi.org/10.1016/j.jmb.2013.05.007
  • Primary Citation Related Structures: 
    4DTE, 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 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.

Macromolecule Content 

  • Total Structure Weight: 43.19 kDa 
  • Atom Count: 3,309 
  • Modeled Residue Count: 370 
  • Deposited Residue Count: 386 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasminogen activator inhibitor 1386Oncorhynchus mykissMutation(s): 0 
Gene Names: serpine1
UniProt
Find proteins for I3WWD7 (Oncorhynchus mykiss)
Explore I3WWD7 
Go to UniProtKB:  I3WWD7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3WWD7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.218 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.065α = 90
b = 56.471β = 93.88
c = 59.75γ = 90
Software Package:
Software NamePurpose
MAR345data collection
xia2data scaling
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations