4RMS

Crystal structure of the D53N Beta-2 Microglobulin mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Decoding the Structural Bases of D76N 2-Microglobulin High Amyloidogenicity through Crystallography and Asn-Scan Mutagenesis.

de Rosa, M.Barbiroli, A.Giorgetti, S.Mangione, P.P.Bolognesi, M.Ricagno, S.

(2015) Plos One 10: e0144061-e0144061

  • DOI: 10.1371/journal.pone.0144061
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • D76N is the first natural variant of human β-2 microglobulin (β2m) so far identified. Contrary to the wt protein, this mutant readily forms amyloid fibres in physiological conditions, leading to a systemic and severe amyloidosis. Although the Asp76As ...

    D76N is the first natural variant of human β-2 microglobulin (β2m) so far identified. Contrary to the wt protein, this mutant readily forms amyloid fibres in physiological conditions, leading to a systemic and severe amyloidosis. Although the Asp76Asn mutant has been extensively characterized, the molecular bases of its instability and aggregation propensity remain elusive. In this work all Asp residues of human β2m were individually substituted to Asn; D-to-N mutants (D34N, D38N, D53N, D59N, D96N and D98N) were characterised in terms of thermodynamic stability and aggregation propensity. Moreover, crystal structures of the D38N, D53N, D59N and D98N variants were solved at high-resolution (1.24-1.70 Å). Despite showing some significant variations in their thermal stabilities, none showed the dramatic drop in melting temperature (relative to the wt protein) as observed for the pathogenic mutant. Consistently, none of the variants here described displayed any increase in aggregation propensity under the experimental conditions tested. The crystal structures confirmed that D-to-N mutations are generally well tolerated, and lead only to minor reorganization of the side chains in close proximity of the mutated residue. D38N is the only exception, where backbone readjustments and a redistribution of the surface electrostatic charges are observed. Overall, our results suggest that neither removing negative charges at sites 34, 38, 53, 59, 96 and 98, nor the difference in β2m pI, are the cause of the aggressive phenotype observed in D76N. We propose that the dramatic effects of the D76N natural mutation must be linked to effects related to the crucial location of this residue within the β2m fold.


    Organizational Affiliation

    Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università di Milano, Via Celoria 2, 20133, Milano, Italy.,CIMAINA and CNR-Istituto di Biofisica, c/o Università di Milano, Via Celoria 26, 20133, Milano, Italy.,Dipartimento di Medicina Molecolare, Istituto di Biochimica "A. Castellani", Università di Pavia, Via Taramelli 3/b, 27100, Pavia, Italy.,Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
A
100Homo sapiensMutation(s): 1 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.191 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.020α = 90.00
b = 28.900β = 101.93
c = 67.155γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
MxCuBEdata collection
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references