4RMU

Crystal structure of the D76E Beta-2 Microglobulin mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity.

Le Marchand, T.de Rosa, M.Salvi, N.Sala, B.M.Andreas, L.B.Barbet-Massin, E.Sormanni, P.Barbiroli, A.Porcari, R.Sousa Mota, C.de Sanctis, D.Bolognesi, M.Emsley, L.Bellotti, V.Blackledge, M.Camilloni, C.Pintacuda, G.Ricagno, S.

(2018) Nat Commun 9: 1658-1658

  • DOI: 10.1038/s41467-018-04078-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate ...

    Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of β2m by X-ray crystallography, solid-state NMR, and molecular dynamics simulations to unveil the effects of the D76N mutation. Taken together, our data highlight the presence of minor disordered substates in crystalline β2m. The destabilization of the outer strands of D76N β2m accounts for the increased aggregation propensity. Furthermore, the computational modeling reveals a network of interactions with residue D76 as a keystone: this model allows predicting the stability of several point mutants. Overall, our study shows how the study of intrinsic dynamics in crystallo can provide crucial answers on protein stability and aggregation propensity. The comprehensive approach here presented may well be suited for the study of other folded amyloidogenic proteins.


    Organizational Affiliation

    Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133, Milano, Italy.,Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy. carlo.camilloni@unimi.it.,Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133, Milano, Italy.,ESRF - The European Synchrotron, 38043, Grenoble, France.,Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK.,Institut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France.,Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy. stefano.ricagno@unimi.it.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France. guido.pintacuda@ens-lyon.fr.




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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.401α = 90.00
b = 28.866β = 124.17
c = 57.870γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
MxCuBEdata collection
MOSFLMdata reduction
PHENIXrefinement

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: 2018-06-27
    Type: Data collection, Database references