5XP1

Structure of monomeric mutant of REI immunoglobulin light chain variable domain crystallized at pH 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5B3C - determined by Mine, S., Nakamura, T., Uegaki, K., Hamada, D., Kobayashi, Y.  

Literature

Heat-induced native dimerization prevents amyloid formation by variable domain from immunoglobulin light-chain REI

Nawata, M.Tsutsumi, H.Kobayashi, Y.Unzai, S.Mine, S.Nakamura, T.Uegaki, K.Kamikubo, H.Kataoka, M.Hamada, D.

(2017) FEBS J. 284: 3114-3127

  • DOI: 10.1111/febs.14181
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amyloid light-chain (AL) amyloidosis is a protein-misfolding disease characterized by accumulation of immunoglobulin light chains (LCs) into amyloid fibrils. Dimerization of a full length or variable domain (V <sub>L </sub> ) of LC serves to stabiliz ...

    Amyloid light-chain (AL) amyloidosis is a protein-misfolding disease characterized by accumulation of immunoglobulin light chains (LCs) into amyloid fibrils. Dimerization of a full length or variable domain (V L ) of LC serves to stabilize the native state and prevent the formation of amyloid fibrils. We here analyzed the thermodynamic properties of dimerization and unfolding reactions by nonamyloidogenic V L from REI LC or its monomeric Y96K mutant using sedimentation velocity and circular dichroism. The data indicate that the equilibrium shifts to native dimerization for wild-type REI V L by elevating temperature due to the negative enthalpy change for dimer dissociation (-81.2 kJ·mol -1 ). The Y96K mutation did not affect the stability of the monomeric native state but increased amyloidogenicity. These results suggest that the heat-induced native homodimerization is the major factor preventing amyloid formation by wild-type REI V L . Heat-induced native oligomerization may be an efficient strategy to avoid the formation of misfolded aggregates particularly for thermostable proteins that are used at elevated temperatures under conditions where other proteins tend to misfold.


    Organizational Affiliation

    Protein Design Laboratory, Yokohama City University, Japan.,Laboratory of Bioenergetics and Biophysics, Nara Institute of Science and Technology (NAIST), Ikoma, Japan.,Center for Applied Structural Science (CASS), Kobe University, Japan.,Graduate School of Medicine, Kobe University, Japan.,Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu, Japan.,Graduate School of Engineering, Kobe University, Japan.,National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin kappa variable 1D-33
A, B, C, D, E, F, G, H
109Homo sapiensMutation(s): 0 
Gene Names: IGKV1D-33
Find proteins for P01593 (Homo sapiens)
Go to UniProtKB:  P01593
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.257 
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 130.760α = 90.00
b = 130.760β = 90.00
c = 92.140γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
iMOSFLMdata reduction
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan26440076
JSPSJapan23107721

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references