4RMS

Crystal structure of the D53N Beta-2 Microglobulin mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.197 

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:  
    4RMQ, 4RMR, 4RMS, 4RMT

  • 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 Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinA100Homo sapiensMutation(s): 1 
Gene Names: B2MCDABP0092HDCMA22PNM_004048
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.197 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.02α = 90
b = 28.9β = 101.93
c = 67.155γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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