4FXL | pdb_00004fxl

Crystal structure of the D76N Beta-2 Microglobulin mutant

• PDB DOI: https://doi.org/10.2210/pdb4FXL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-07-03 Released: 2012-08-15 
• Deposition Author(s): Ricagno, S., Bellotti, V., Pepys, M.B., Stoppini, M., Bolognesi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.186 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

Hereditary systemic amyloidosis due to Asp76Asn variant beta-2-microglobulin.

Valleix, S., Gillmore, J.D., Bridoux, F., Mangione, P.P., Dogan, A., Nedelec, B., Boimard, M., Touchard, G., Goujon, J.M., Lacombe, C., Lozeron, P., Adams, D., Lacroix, C., Maisonobe, T., Plante-Bordeneuve, V., Vrana, J.A., Theis, J.D., Giorgetti, S., Porcari, R., Ricagno, S., Bolognesi, M., Stoppini, M., Delpech, M., Pepys, M.B., Hawkins, P.N., Bellotti, V.

(2012) N Engl J Med 366: 2276-2283

• PubMed: 22693999 
• DOI: https://doi.org/10.1056/NEJMoa1201356
• Primary Citation Related Structures: 
  4FXL


• PubMed Abstract: 
  

  We describe a kindred with slowly progressive gastrointestinal symptoms and autonomic neuropathy caused by autosomal dominant, hereditary systemic amyloidosis. The amyloid consists of Asp76Asn variant β(2)-microglobulin. Unlike patients with dialysis-related amyloidosis caused by sustained high plasma concentrations of wild-type β(2)-microglobulin, the affected members of this kindred had normal renal function and normal circulating β(2)-microglobulin values. The Asp76Asn β(2)-microglobulin variant was thermodynamically unstable and remarkably fibrillogenic in vitro under physiological conditions. Previous studies of β(2)-microglobulin aggregation have not shown such amyloidogenicity for single-residue substitutions. Comprehensive biophysical characterization of the β(2)-microglobulin variant, including its 1.40-Å, three-dimensional structure, should allow further elucidation of fibrillogenesis and protein misfolding.

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Organizational Affiliation: 
• Laboratoire de Biochimie et de Génétique Moléculaire, Université Paris-Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris, Assistance Public–Hôpitaux de Paris (AP-HP), Paris, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 12.07 kDa 
• Atom Count: 982 
• Modeled Residue Count: 100 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	A	100	Homo sapiens	Mutation(s): 1  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.186 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.22	α = 90
b = 28.42	β = 126.54
c = 52.26	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Ricagno, S., Bellotti, V., Pepys, M.B., Stoppini, M., Bolognesi, M.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-27
  Changes: Structure summary