2Q20

Structure of the germline Vk1 O18/O8 light chain variable domain homodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Altered dimer interface decreases stability in an amyloidogenic protein.

Baden, E.M.Owen, B.A.Peterson, F.C.Volkman, B.F.Ramirez-Alvarado, M.Thompson, J.R.

(2008) J.Biol.Chem. 283: 15853-15860

  • DOI: 10.1074/jbc.M705347200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amyloidoses are devastating and currently incurable diseases in which the process of amyloid formation causes fatal cellular and organ damage. The molecular mechanisms underlying amyloidoses are not well known. In this study, we address the structura ...

    Amyloidoses are devastating and currently incurable diseases in which the process of amyloid formation causes fatal cellular and organ damage. The molecular mechanisms underlying amyloidoses are not well known. In this study, we address the structural basis of immunoglobulin light chain amyloidosis, which results from deposition of light chains produced by clonal plasma cells. We compare light chain amyloidosis protein AL-09 to its wild-type counterpart, the kappaI O18/O8 light chain germline. Crystallographic studies indicate that both proteins form dimers. However, AL-09 has an altered dimer interface that is rotated 90 degrees from the kappaI O18/O8 dimer interface. The three non-conservative mutations in AL-09 are located within the dimer interface, consistent with their role in the decreased stability of this amyloidogenic protein. Moreover, AL-09 forms amyloid fibrils more quickly than kappaI O18/O8 in vitro. These results support the notion that the increased stability of the monomer and delayed fibril formation, together with a properly formed dimer, may be protective against amyloidogenesis. This could open a new direction into rational drug design for amyloidogenic proteins.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vk1 O18/O8 germline light chain variable domain
A, B
109Homo sapiensMutation(s): 0 
Gene Names: IGKV1-33
Find proteins for P01594 (Homo sapiens)
Go to UniProtKB:  P01594
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.119 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 74.265α = 90.00
b = 74.265β = 90.00
c = 99.051γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
SBC-Collectdata collection
PHASERphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description