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 6M1B | pdb_00006m1b

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 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6M1B

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 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.

Macromolecule Content 

  • Total Structure Weight: 12.25 kDa 
  • Atom Count: 884 
  • Modeled Residue Count: 100 
  • Deposited Residue Count: 100 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 1 
Gene Names: B2M, CDABP0092, HDCMA22P
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 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.205 (Depositor) 
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