4K07

Crystal structure of the amyloid-forming immunoglobulin AL-103 cis-proline 95 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kinetic control in protein folding for light chain amyloidosis and the differential effects of somatic mutations.

Blancas-Mejia, L.M.Tischer, A.Thompson, J.R.Tai, J.Wang, L.Auton, M.Ramirez-Alvarado, M.

(2014) J.Mol.Biol. 426: 347-361

  • DOI: 10.1016/j.jmb.2013.10.016

  • PubMed Abstract: 
  • Light chain amyloidosis is a devastating disease where immunoglobulin light chains form amyloid fibrils, resulting in organ dysfunction and death. Previous studies have shown a direct correlation between the protein thermodynamic stability and the pr ...

    Light chain amyloidosis is a devastating disease where immunoglobulin light chains form amyloid fibrils, resulting in organ dysfunction and death. Previous studies have shown a direct correlation between the protein thermodynamic stability and the propensity for amyloid formation for some proteins involved in light chain amyloidosis. Here we investigate the effect of somatic mutations on protein stability and in vitro fibril formation of single and double restorative mutants of the protein AL-103 compared to the wild-type germline control protein. A scan rate dependence and hysteresis in the thermal unfolding and refolding was observed for all proteins. This indicates that the unfolding/refolding reaction is kinetically determined with different kinetic constants for unfolding and refolding even though the process remains experimentally reversible. Our structural analysis of AL-103 and AL-103 delP95aIns suggests a kinetic coupling of the unfolding/refolding process with cis-trans prolyl isomerization. Our data reveal that the deletion of proline 95a (AL-103 delP95aIns), which removes the trans-cis di-proline motif present in the patient protein AL-103, results in a dramatic increment in the thermodynamic stability and a significant delay in fibril formation kinetics with respect to AL-103. Fibril formation is pH dependent; all proteins form fibrils at pH2; reactions become slower and more stochastic as the pH increases up to pH7. Based on these results, we propose that, in addition to thermodynamic stability, kinetic stability (possibly influenced by the presence of cis proline 95a) plays a major role in the AL-103 amyloid fibril formation process.


    Organizational Affiliation

    Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA; Division of Hematology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA. Electronic address: ramirezalvarado.marina@mayo.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amyloidogenic immunoglobulin light chain protein AL-103
A, B, C, D, E, F, G, H, I, J
129Homo sapiensMutation(s): 0 
Gene Names: IGKV1-33
Find proteins for P01594 (Homo sapiens)
Go to UniProtKB:  P01594
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 159.910α = 90.00
b = 200.334β = 90.00
c = 40.056γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data collection
PHENIXphasing
PHENIXmodel building
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references
  • Version 1.2: 2014-01-22
    Type: Database references