2Z9T | pdb_00002z9t

Crystal structure of the human beta-2 microglobulin mutant W60G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.214 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2Z9T

This is version 1.4 of the entry. See complete history

Literature

The controlling roles of Trp60 and Trp95 in beta2-microglobulin function, folding and amyloid aggregation properties

Esposito, G.Ricagno, S.Corazza, A.Rennella, E.Gumral, D.Mimmi, M.C.Betto, E.Pucillo, C.E.M.Fogolari, F.Viglino, P.Raimondi, S.Giorgetti, S.Bolognesi, B.Merlini, G.Stoppini, M.Bolognesi, M.Bellotti, V.

(2008) J Mol Biology 378: 885-895

  • DOI: https://doi.org/10.1016/j.jmb.2008.03.002
  • Primary Citation Related Structures: 
    2VB5, 2Z9T

  • PubMed Abstract: 

    Amyloidosis associated to hemodialysis is caused by persistently high beta(2)-microglobulin (beta(2)m) serum levels. beta(2)m is an intrinsically amyloidogenic protein whose capacity to assemble into amyloid fibrils in vitro and in vivo is concentration dependent; no beta(2)m genetic variant is known in the human population. We investigated the roles of two evolutionary conserved Trp residues in relation to beta(2)m structure, function and folding/misfolding by means of a combined biophysical and functional approach. We show that Trp60 plays a functional role in promoting the association of beta(2)m in class I major histocompatibility complex; it is exposed to the solvent at the apex of a protein loop in order to accomplish such function. The Trp60-->Gly mutation has a threefold effect: it stabilizes beta(2)m, inhibits beta(2)m amyloidogenic propensity and weakens the interaction with the class I major histocompatibility complex heavy chain. On the contrary, Trp95 is buried in the beta(2)m core; the Trp95-->Gly mutation destabilizes the protein, which is unfolded in solution, yielding nonfibrillar beta(2)m aggregates. Trp60 and Trp95 therefore play differential and complementary roles in beta(2)m, being relevant for function (Trp60) and for maintenance of a properly folded structure (Trp95) while affecting in distinct ways the intrinsic propensity of wild-type beta(2)m towards self-aggregation into amyloid fibrils.


  • Organizational Affiliation
    • Department of Biomedical Science and Technology, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy.

Macromolecule Content 

  • Total Structure Weight: 11.75 kDa 
  • Atom Count: 973 
  • 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: NM_004048
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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.214 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.678α = 90
b = 29.014β = 125.26
c = 59.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary