Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor.

The Ig new antigen receptors (IgNARs) are single-domain antibodies found in the serum of sharks. Here, we report 2.2- and 2.8-A structures of the type 2 IgNAR variable domains 12Y-1 and 12Y-2. Structural features include, first, an Ig superfamily topology transitional between cell adhesion molecules, antibodies, and T cell receptors; and, second, a vestigial complementarity-determining region 2 at the "bottom" of the molecule, apparently discontinuous from the antigen-binding paratope and similar to that observed in cell adhesion molecules. Thus, we suggest that IgNARs originated as cell-surface adhesion molecules coopted to the immune repertoire and represent an evolutionary lineage independent of variable heavy chain/variable light chain type antibodies. Additionally, both 12Y-1 and 12Y-2 form unique crystallographic dimers, predominantly mediated by main-chain framework interactions, which represent a possible model for primordial cell-based interactions. Unusually, the 12Y-2 complementarity-determining region 3 also adopts an extended beta-hairpin structure, suggesting a distinct selective advantage in accessing cryptic antigenic epitopes.

Electron density in the sodium vanadium oxide bronze beta-Na(x)V(2)O(5) at 9 K.

The crystal structure and electron density in sodium vanadium oxide bronze, beta-Na(x)V(2)O(5) [x = 0.282 (3)], have been studied by accurate Mo Kalpha X-ray diffraction measurements at 9.6 (3) K. No noticeable difference in the crystal structures at room temperature and 9.6 K has been observed. No superstructure reflections, previously found by Kanai, Kagoshima & Nagasawa [(1982), J. Phys. Soc. Jpn, 51, 697-698], have been detected at low temperature. Analysis of the deformation electron density has revealed the presence of the quasi-two-dimensional sheets of the -V-O-V-O- bonds in the structure. The electron density in the different chemical bonds within each of the three crystallographically independent VO(6) polyhedra noticeably varies, although there is no clear evidence that the three crystallographically independent V atoms have different valence states.

Synchrotron X-ray analysis of the electron density in CoF2 and ZnF2.

Accurate structure factors for small crystals of the rutile-type structures CoF(2), cobalt difluoride, and ZnF(2), zinc difluoride, have been measured with focused lambda = 0.8400 (2) A synchrotron X-radiation at room temperature. Phenomenological structural trends across the full series of rutile-type transition metal difluorides are analysed, showing the importance of the metal atom in the degree of distortion of the metal-F(6) octahedra in these structures. Multipole models reveal strong asphericities in the electron density surrounding the transition metals, which are consistent with expectations from crystal field theory and the structural trends in these compounds. Transition metal 3d-orbital populations were computed from the multipole refinement parameters, showing significant repopulation of orbitals compared with the free atom, particularly for CoF(2).

Synchrotron X-ray analysis of RbTiOAsO4.

Structure factors for rubidium oxotitanium arsenate, RbTiOAsO(4), were measured at 293 K with focused synchrotron X-radiation [lambda = 0.7500 (9) A] using a fast avalanche photodiode counter. The accurate synchrotron single-crystal data are of sufficient quality and resolution to detect the splitting positions of the Rb cations at room temperature. Strong accumulation of the Deltarho difference charge density near the Rb atoms at a distance of approximately 0.5 A in the -c direction can be attributed to the partial occupancy of additional sites related by pseudosymmetry. This type of static and/or dynamic disorder is temperature-dependent and seems to be universal for the KTiOPO(4) family of compounds. The best modelling of the experimental data was obtained with the Rb atom in split positions described within the harmonic approximation and the multipole functions for the other atoms. The Deltarho density features in the Ti-O and As-O covalent bonds can be related to the linear and non-linear susceptibility using bond-polarization theory. The charge-density maps reflect the anisotropy of non-linear susceptibility, which is larger for directions where locally antisymmetric components of Deltarho are strong.

Synchrotron X-ray imaging of the electron density in RFeO3 (R = Y, Ho) using an APD detector.

Structure factors for small hydrothermally grown yttrium and holmium orthoferrites, RFeO(3) (R = Y, Ho), were measured with focused synchrotron radiation at wavelengths of 0.70 and 0.84 A using both scintillation and high-speed avalanche photodiode (APD) detectors. Resulting APD Deltarho images showed striking correlations between aspherical electron densities around Fe and rare-earth metals. Approximate high symmetry in the Deltarho images indicates that cations deform the electron density far more strongly than the O atoms. The Ho-Fe magnetic interactions appear to affect the electron density distribution of the Fe atoms and the magnetic phase transitions. Space group Pnma, orthorhombic, YFeO3 (APD): Mr = 192.76, a = 5.5931 (3), b = 7.6102 (4), c = 5.2806 (3) A, V = 224.77 (2) A(3), Z = 4, Dx = 5.695 Mg m(-3), mu(0.84) = 15.56 mm(-1), F(000) = 356, T = 293 K, R = 0.045, wR = 0.073, S = 4.83 (9) for 1282 unique reflections; HoFeO3 (APD): Mr = 268.78, a = 5.5922 (3), b = 7.6157 (5), c = 5.2798 (3) A, V = 224.86 (2) A(3), Z = 4, D(x) = 7.939 Mg m(-3), mu(0.84) = 61.98 mm(-1), F(000) = 356, T = 293 K, R = 0.036, wR = 0.037, S = 3.07 (6) for 1284 unique reflections.