3DVI

Crystal structure of kappa 1 amyloidogenic light chain variable domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural alterations within native amyloidogenic immunoglobulin light chains.

Randles, E.G.Thompson, J.R.Martin, D.J.Ramirez-Alvarado, M.

(2009) J.Mol.Biol. 389: 199-210

  • DOI: 10.1016/j.jmb.2009.04.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amyloid diseases are characterized by the misfolding of a precursor protein that leads to amyloid fibril formation. Despite the fact that there are different precursors, some commonalities in the misfolding mechanism are thought to exist. In light ch ...

    Amyloid diseases are characterized by the misfolding of a precursor protein that leads to amyloid fibril formation. Despite the fact that there are different precursors, some commonalities in the misfolding mechanism are thought to exist. In light chain amyloidosis (AL), the immunoglobulin light chain forms amyloid fibrils that deposit in the extracellular space of vital organs. AL proteins are thermodynamically destabilized compared to non-amyloidogenic proteins and some studies have linked this instability to increased fibril formation rates. Here we present the crystal structures of two highly homologous AL proteins, AL-12 and AL-103. This structural study shows that these proteins retain the canonical germ line dimer interface. We highlight important structural alterations in two loops flanking the dimer interface and correlate these results with the somatic mutations present in AL-12 and AL-103. We suggest that these alterations are informative structural features that are likely contributing to protein instability that leads to conformational changes involved in the initial events of amyloid formation.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amyloidogenic light chain variable domain AL-103
A
109N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.189 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.020α = 90.00
b = 47.020β = 90.00
c = 103.356γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
CrystalCleardata collection
PHASERphasing
REFMACrefinement
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance