ISDA

Deposition Date 2010-03-07

Release Date 2011-01-19

Last Version Date 2024-10-16

Entry Detail

PDB ID:

2X89

Keywords:

IMMUNE SYSTEM

Title:

Structure of the Beta2_microglobulin involved in amyloidogenesis

Biological Source:

Source Organism:

CAMELUS DROMEDARIUS (Taxon ID: 9838)
HOMO SAPIENS (Taxon ID: 9606)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.16 Å

R-Value Free:

0.26

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ANTIBODY
Chain IDs:A, B, C
Chain Length:128
Number of Molecules:3
Biological Source:CAMELUS DROMEDARIUS

UniProt ID:A2KD59 Pfam ID:PF07686

Protein Blast

Polymer Type:polypeptide(L)
Molecule:BETA-2-MICROGLOBULIN
Gene (Uniprot):B2M
Chain IDs:D, E, F, G
Chain Length:94
Number of Molecules:4
Biological Source:HOMO SAPIENS

UniProt ID:P61769 Pfam ID:PF07654

Primary Citation

Atomic Structure of a Nanobody-Trapped Domain-Swapped Dimer of an Amyloidogenic {Beta}2-Microglobulin Variant.

Domanska, K, Vanderhaegen, S, Srinivasan, V, Pardon, E, Dupeux, F, Marquez, J.A, Giorgetti, S, Stoppini, M, Wyns, L, Bellotti, V, Steyaert, J.Show

Proc.Natl.Acad.Sci.USA 108 1314 ? (2011)

PMID: 21220305 DOI: 10.1073/PNAS.1008560108

Abstact

Atomic-level structural investigation of the key conformational intermediates of amyloidogenesis remains a challenge. Here we demonstrate the utility of nanobodies to trap and characterize intermediates of β2-microglobulin (β2m) amyloidogenesis by X-ray crystallography. For this purpose, we selected five single domain antibodies that block the fibrillogenesis of a proteolytic amyloidogenic fragment of β2m (ΔN6β2m). The crystal structure of ΔN6β2m in complex with one of these nanobodies (Nb24) identifies domain swapping as a plausible mechanism of self-association of this amyloidogenic protein. In the swapped dimer, two extended hinge loops--corresponding to the heptapetide NHVTLSQ that forms amyloid in isolation--are unmasked and fold into a new two-stranded antiparallel β-sheet. The β-strands of this sheet are prone to self-associate and stack perpendicular to the direction of the strands to build large intermolecular β-sheets that run parallel to the axis of growing oligomers, providing an elongation mechanism by self-templated growth.

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