3LOW

Crystal structure of Beta 2 Microglobulin domain-swapped dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Beta2-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages.

Liu, C.Sawaya, M.R.Eisenberg, D.

(2011) Nat Struct Mol Biol 18: 49-55

  • DOI: 10.1038/nsmb.1948
  • Primary Citation of Related Structures:  
    3LOW, 3LOZ

  • PubMed Abstract: 
  • β₂-microglobulin (β₂m) is the light chain of the type I major histocompatibility complex. It deposits as amyloid fibrils within joints during long-term hemodialysis treatment. Despite the devastating effects of dialysis-related amyloidosis, full unde ...

    β₂-microglobulin (β₂m) is the light chain of the type I major histocompatibility complex. It deposits as amyloid fibrils within joints during long-term hemodialysis treatment. Despite the devastating effects of dialysis-related amyloidosis, full understanding of how fibrils form from soluble β₂m remains elusive. Here we show that β₂m can oligomerize and fibrillize via three-dimensional domain swapping. Isolating a covalently bound, domain-swapped dimer from β₂m oligomers on the pathway to fibrils, we were able to determine its crystal structure. The hinge loop that connects the swapped domain to the core domain includes the fibrillizing segment LSFSKD, whose atomic structure we also determined. The LSFSKD structure reveals a class 5 steric zipper, akin to other amyloid spines. The structures of the dimer and the zipper spine fit well into an atomic model for this fibrillar form of β₂m, which assembles slowly under physiological conditions.


    Organizational Affiliation

    University of California Los Angeles-United States Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinAB100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.721α = 90
b = 29.162β = 97.49
c = 67.715γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-02-04 
  • Released Date: 2010-12-08 
  • Deposition Author(s): Liu, C., Eisenberg, D.

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-09-19
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description