PDBsum entry 2d4f

Immune system

PDB id: 2d4f

Contents

Protein chain

98 a.a. *

Metals

_NA

Waters ×65

* Residue conservation analysis

PDB id:

2d4f

Name:

Immune system

Title:

The crystal structure of human beta2-microglobulin

Structure:

Beta-2-microglobulin. Chain: a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.208 R-free: 0.233

Authors:

K.Iwata,T.Matsuura,A.Nakagawa,Y.Goto

Key ref:

M.Kihara et al. (2006). Conformation of amyloid fibrils of beta2-microglobulin probed by tryptophan mutagenesis. J Biol Chem, 281, 31061-31069. PubMed id: 16901902 DOI: 10.1074/jbc.M605358200

Date:

18-Oct-05 Release date: 08-Aug-06

Protein chain

P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens

Seq: 119 a.a.

Struc: 98 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.M605358200

J Biol Chem 281:31061-31069 (2006)

PubMed id: 16901902

Conformation of amyloid fibrils of beta2-microglobulin probed by tryptophan mutagenesis.

M.Kihara, E.Chatani, K.Iwata, K.Yamamoto, T.Matsuura, A.Nakagawa, H.Naiki, Y.Goto.

ABSTRACT

Beta2-microglobulin (beta2-m), a protein responsible for dialysis-related amyloidosis, adopts an immunoglobulin domain fold in its native state. Although beta2-m has Trp residues at positions 60 and 95, both are located near the surface of the domain. Hence, beta2-m does not have a conserved Trp common to other immunoglobulin domains, which is buried in close proximity to the disulfide bond. To study the structure of amyloid fibrils in relation to their native fold, we prepared a series of Trp mutants. Trp60 and Trp95 were both replaced with Phe, and a single Trp was introduced at various positions. Among various mutants, W39-beta2-m, in which a Trp was introduced at the position corresponding to the conserved Trp, exhibited a remarkable quenching of fluorescence in the native state, as observed for other immunoglobulin domains. An x-ray structural analysis revealed that W39-beta2-m assumes the native fold with Trp39 located in the vicinity of the disulfide bond. Comparison of the fluorescence spectra of various mutants for the native and fibrillar forms indicated that, while the Trp residues introduced in the middle of the beta2-m sequence tend to be buried in the fibrils, those located in the C-terminal region are more exposed. In addition, the fluorescence spectra of fibrils prepared at pH 2.5 and 7.0 revealed a large difference in the fluorescence intensity for W60-beta2-m, implying a major structural difference between them.

Selected figure(s)

Figure 1.
FIGURE 1. Structure of 2-m and location of mutations introduced. A, amino acid sequence. Trp^60 and Trp^95 are indicated in red and orange, respectively. Residues mutated to Trp are Leu^39 (green), Ser^33 (cyan), Val^49 (blue), and Tyr^78 (purple). A Met is always present at the N terminus of all the 2-ms, which is indicated as M0. B, schematic structure. Side chains of Trp^60 and Trp^95 and the residues mutated to Trp are indicated with the same colors as in A. Secondary structures are indicated by hydrogen bonds (A) and the numbering of -strands (A and B). The schematic structure was produced using MOLMOL (43) with our structure (PDB code 2D4F).

Figure 7.
FIGURE 7. AFM and total internal reflection fluorescence microscopic images of amyloid fibrils. A-D, AFM images of amyloid fibrils of wild-type 2-m (A and B) and W39- 2-m (C and D) prepared at pH 2.5 (A and C)or pH 7.0 (B and D). E and F, total internal reflection fluorescence microscopic images of W39- 2-m prepared at pH 2.5 (E)or pH 7.0 (F). The side of an AFM image is 5-µm long and that of a fluorescence micrograph is 20 µm.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 31061-31069) copyright 2006.

Figures were selected by an automated process.