PDBsum entry 2omn

Immune system

PDB id: 2omn

Contents

Protein chains

217 a.a. *

Ligands

SO4 ×3

IPH

Waters ×98

* Residue conservation analysis

PDB id:

2omn

Name:

Immune system

Title:

Bence jones kwr protein- immunoglobulin light chain dimer, p4(3)2(1)2 crystal form

Structure:

Bence jones kwr protein - immunoglobulin light chain. Chain: a, b

Source:

Homo sapiens. Human. Organism_taxid: 9606. Strain: kwr. Other_details: urine

Resolution:

2.20Å R-factor: 0.226 R-free: 0.283

Authors:

D.L.Makino,S.B.Larson,A.Mcpherson

Key ref:

D.L.Makino et al. (2007). Bence Jones KWR protein structures determined by X-ray crystallography. Acta Crystallogr D Biol Crystallogr, 63, 780-792. PubMed id: 17582169 DOI: 10.1107/S0907444907021981

Date:

22-Jan-07 Release date: 17-Jul-07

Protein chains

No UniProt id for this chain

Struc: 217 a.a.

DOI no: 10.1107/S0907444907021981

Acta Crystallogr D Biol Crystallogr 63:780-792 (2007)

PubMed id: 17582169

Bence Jones KWR protein structures determined by X-ray crystallography.

D.L.Makino, A.H.Henschen-Edman, S.B.Larson, A.McPherson.

ABSTRACT

A Bence Jones protein isolated in the early 1960s from a patient (initials KWR) suffering from plasma-cell dyscrasia was crystallized and its structure was analyzed in four different unit cells by X-ray diffraction. The final models of the molecule in all crystal forms were virtually the same, although the elbow angles relating the constant and variable domains of the Bence Jones dimers varied over a range of 10 degrees. The tetragonal form had an R factor of 22.6% and an R(free) of 28.3% at 2.2 A resolution. Phosphate or sulfate ions (depending on the crystallization conditions) were found in the antigen-combining sites in all crystals, as well as an unidentified ligand tightly bound in the hydrophobic 'deep pocket' beneath the antigen-binding site. The ligand was treated as a phenol molecule. Two trigonal crystal forms were among those solved. One was grown at pH 4.0 and the other was only obtained after sitting for more than eight months at room temperature. The latter crystal was composed of molecules that were degraded in their constant domains. Both low pH and proteolytic degradation of constant domains are known to promote the polymerization of some Bence Jones proteins into amyloid fibrils. Indeed, in both trigonal crystal forms the molecules are organized with pseudo-hexagonal symmetry about the unique crystallographic axes in a manner suggestive of such fibrils. The arrangement of Bence Jones dimers is also consistent with other observations regarding Bence Jones amyloid-fibril structure and current models.

Selected figure(s)

Figure 6.
Figure 6 Sulfate-ion and phosphate-ion interactions in the main cavity of what would be the antigen-binding site of a Fab. The elbow region of the P3[2]21 crystal shows the location of the phenol molecule and a phosphate also observed in that region. A symmetry-related molecule is indicated in gray.

Figure 8.
Figure 8 Detail of the lateral interactions between neighboring variable domains in the P3[1]21 crystal. (a) Interaction between adjacent -strands from two variable domains of chains B and D forms an extended -sheet; (b) lateral interactions between neighboring variable domains of chains A and C.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 780-792) copyright 2007.

Figures were selected by an automated process.