3CIQ

A regulatable switch mediates self-association in an immunoglobulin fold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A regulatable switch mediates self-association in an immunoglobulin fold.

Calabrese, M.F.Eakin, C.M.Wang, J.M.Miranker, A.D.

(2008) Nat.Struct.Mol.Biol. 15: 965-971


  • PubMed Abstract: 
  • Beta-2 microglobulin (beta2m) is a globular protein that self-associates into fibrillar amyloid deposits in patients undergoing hemodialysis therapy. Formation of these beta-sheet-rich assemblies is a fundamental property of polypeptides that can be ...

    Beta-2 microglobulin (beta2m) is a globular protein that self-associates into fibrillar amyloid deposits in patients undergoing hemodialysis therapy. Formation of these beta-sheet-rich assemblies is a fundamental property of polypeptides that can be triggered by diverse conditions. For beta2m, oligomerization into pre-amyloidogenic states occurs in specific response to coordination by Cu2+. Here we report the basis for this self-association at atomic resolution. Metal is not a direct participant in the molecular interface. Rather, binding results in distal alterations enabling the formation of two new surfaces. These interact to form a closed hexameric species. The origins of this include isomerization of a buried and conserved cis-proline previously implicated in the beta2m aggregation pathway. The consequences of this isomerization are evident and reveal a molecular basis for the conversion of this robust monomeric protein into an amyloid-competent state.


    Related Citations: 
    • A native to amyloidogenic transition regulated by a backbone trigger
      Eakin, C.M.,Berman, A.J.,Miranker, A.D.
      (2006) Nat.Struct.Mol.Biol. 13: 202
    • Formation of a stable oligomer of beta-2 microglobulin requires only transient encounter with Cu(II)
      Calabrese, M.F.,Miranker, A.D.
      (2007) J.Mol.Biol. 367: 1


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
A, B, C, D, E, F, G, H, I, J, K, L
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
TLA
Query on TLA

Download SDF File 
Download CCD File 
G
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.225 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 67.594α = 104.38
b = 68.047β = 94.15
c = 96.218γ = 117.77
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance