6M1B

A new V27M variant of beta 2 microglobulin induced amyloidosis in a patient with long-term hemodialysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Dialysis-related amyloidosis associated with a novel beta 2 -microglobulin variant.

Mizuno, H.Hoshino, J.So, M.Kogure, Y.Fujii, T.Ubara, Y.Takaichi, K.Nakaniwa, T.Tanaka, H.Kurisu, G.Kametani, F.Nakagawa, M.Yoshinaga, T.Sekijima, Y.Higuchi, K.Goto, Y.Yazaki, M.

(2021) Amyloid 28: 42-49

  • DOI: https://doi.org/10.1080/13506129.2020.1813097
  • Primary Citation of Related Structures:  
    6M1B

  • PubMed Abstract: 

    Till date, there had been no reported case of dialysis-related amyloidosis (DRA) associated with a β 2 -microglobulin variant. We report here a 41-year-old haemodialysis patient with systemic amyloidosis, exhibiting macroglossia and swelling salivary glands, uncommon clinical manifestations for DRA. Molecular analysis showed that the patient had a new variant of β 2 -microglobulin (V27M). Extracted amyloid protein was predominantly composed of variant β 2 -microglobulin. In vitro analysis revealed that this variant β 2 -microglobulin had a strong amyloidogenic propensity, probably owing to the decreased stability caused by a bulky methionine residue. Our data clearly show that V27M variant is amyloidogenic and this mutation results in unusual clinical manifestations. To date, only one amyloidogenic β 2 -microglobulin variant (D76N) has been reported in non-dialysis patients. It is noteworthy that the V27M and D76N variants show substantial differences in both clinical phenotypes and pathomechanical features. This is the first case of DRA associated with a naturally occurring β 2 -microglobulin variant.


  • Organizational Affiliation

    Nephrology Center, Toranomon Hospital, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 1 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.26α = 90
b = 28.9β = 121.68
c = 54.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary