Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.42 kDa 
• Atom Count: 3679 
• Residue Count: 445 
• Unique protein chains: 2

4KDT

Structure of an early native-like intermediate of beta2-microglobulin amyloidosis

• DOI: 10.2210/pdb4KDT/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Camelidae, Homo sapiens
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-04-25 Released: 2013-08-28 
• Deposition Author(s): Vanderhaegen, S., Fislage, M., Pardon, E., Versees, W., Steyaert, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Literature

Structure of an early native-like intermediate of beta 2-microglobulin amyloidogenesis.

Vanderhaegen, S., Fislage, M., Domanska, K., Versees, W., Pardon, E., Bellotti, V., Steyaert, J.

(2013) Protein Sci 22: 1349-1357

• PubMed: 23904325 
• DOI: 10.1002/pro.2321
• Primary Citation of Related Structures:  
  4KDT


• PubMed Abstract: 
  

To investigate early intermediates of β2-microglobulin (β2m) amyloidogenesis, we solved the structure of β2m containing the amyloidogenic Pro32Gly mutation by X-ray crystallography. One nanobody (Nb24) that efficiently blocks fibril elongation was used as a chaperone to co-crystallize the Pro32Gly β2m monomer under physiological conditions. The complex of P32G β2m with Nb24 reveals a trans peptide bond at position 32 of this amyloidogenic variant, whereas Pro32 adopts the cis conformation in the wild-type monomer, indicating that the cis to trans isomerization at Pro32 plays a critical role in the early onset of β2m amyloid formation.

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Organizational Affiliation: 

Structural Biology Research Centre, VIB, Pleinlaan 2, 1050, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussel, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody24	A, B	134	Camelidae	Mutation(s): 0

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C, D	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.79	α = 90
b = 96.79	β = 90
c = 167.79	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-25 
• Released Date: 2013-08-28 
Deposition Author(s): Vanderhaegen, S., Fislage, M., Pardon, E., Versees, W., Steyaert, J.

Revision History 

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description