Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.03 kDa 
• Atom Count: 1655 
• Modelled Residue Count: 198 
• Deposited Residue Count: 200 
• Unique protein chains: 1

3LOW

Crystal structure of Beta 2 Microglobulin domain-swapped dimer

• DOI: 10.2210/pdb3LOW/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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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 

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

• PubMed: 21131979 
• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	A, B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 59.721	α = 90
b = 29.162	β = 97.49
c = 67.715	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

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