Elizabeth A. Hewat

Structural anomalies, oxygen ordering and superconductivity in oxygen deficient Ba2YCu3Ox

Abstract We report the characterization of series of oxygen deficient Ba2YCu3Ox samples for 7 ≥ x ≥ 6 prepared by Zr gettered annealing at 440°C. Measurements include complete crystal structure analysis at 5 K by powder neutron diffraction, electron microscopy study of the oxygen ordering, and magnetic measurements of the superconducting transitions, with particular attention to the transition widths. The results show for the first time that the 90 K and 60 K plateaus in Tc as a function of oxygen stoichiometry are associated with plateaus in the effective valence of the plane coppers. We also correlate the disappearance of superconductivity for x

The cellular receptor to human rhinovirus 2 binds around the 5-fold axis and not in the canyon: a structural view

Human rhinovirus serotype 2 (HRV2) belongs to the minor group of HRVs that bind to members of the LDL‐receptor family including the very low density lipoprotein (VLDL)‐receptor (VLDL‐R). We have determined the structures of the complex between HRV2 and soluble fragments of the VLDL‐R to 15 Å resolution by cryo‐electron microscopy. The receptor fragments, which include the first three ligand‐binding repeats of the VLDL‐R (V1–3), bind to the small star‐shaped dome on the icosahedral 5‐fold axis. This is in sharp contrast to the major group of HRVs where the receptor site for ICAM‐1 is located at the base of a depression around each 5‐fold axis. Homology models of the three domains of V1–3 were used to explore the virus–receptor interaction. The footprint of VLDL‐R on the viral surface covers the BC‐ and HI‐loops on VP1.

A note on the symmetry and Bi valence of the superconductor Bi2Sr2Ca1Cu2O8

Abstract The sub-structure of Bi 2 Sr 2 Ca 1 Cu 2 O 8 can best be described on a non-centric orthorhombic A2aa cell, which permits the oxygen in the BiO plane to move off the center of the Bi square to approach to within 2.2 A of a pair of Bi atoms. Each Bi then has two close oxygens within the BiO plane, and a third at 2.12 A connecting to the CuO layer. The new structure permits the apparent Bi valence to approach 3+ with a more reasonable Bi-O co-ordination than for earlier approximate structural models. This model satisfies the high resolution neutron data of Bordet et al., while agreeing in part with the co-ordination proposed on chemical grounds by von Schnering et al.

Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: positioning of a highly mobile antigenic loop

Data from cryo‐electron microscopy and X‐ray crystallography have been combined to study the interactions of foot‐and‐mouth disease virus serotype C (FMDV‐C) with a strongly neutralizing monoclonal antibody (mAb) SD6. The mAb SD6 binds to the long flexible GH‐loop of viral protein 1 (VP1) which also binds to an integrin receptor. The structure of the virus–Fab complex was determined to 30 Å resolution using cryo‐electron microscopy and image analysis. The known structure of FMDV‐C, and of the SD6 Fab co‐crystallized with a synthetic peptide corresponding to the GH‐loop of VP1, were fitted to the cryo‐electron microscope density map. The SD6 Fab is seen to project almost radially from the viral surface in an orientation which is only compatible with monovalent binding of the mAb. Even taking into account the mAb hinge and elbow flexibility, it is not possible to model bivalent binding without severely distorting the Fabs. The bound GH‐loop is essentially in what has previously been termed the ‘up’ position in the best fit Fab orientation. The SD6 Fab interacts almost exclusively with the GH‐loop of VP1, making very few other contacts with the viral capsid. The position and orientation of the SD6 Fab bound to FMDV‐C is in accord with previous immunogenic data.

Three-dimensional reconstruction of baculovirus expressed bluetongue virus core-like particles by cryo-electron microscopy

When the viral proteins VP3 and VP7 of bluetongue virus (BTV) are expressed simultaneously in the baculovirus system, core-like particles form spontaneously. The 3-D structure of these core-like particles, determined from cryo-electron micrographs, reveals an icosahedral structure 72.5 nm in diameter with 200 triangular spikes arranged on a T = 13,I lattice; The five spikes around each of the fivefold axes are absent. This is in contrast to the native BTV core particles which have a complete T = 13,I lattice of 260 spikes. The spikes, attributed to VP7 trimers appear as triangular columns 8.0 nm in height with distinct inner and outer domains. The inner shell of the core-like particles, or subcore-like particle, has a T = 1 lattice composed of 60 copies of VP3. The subcore-like particle is noticeably thicker around the fivefold positions. Pores in the subcore-like particle are situated near each of the local sixfold axes, below each six-membered ring of spikes. These pores could allow the passage of metabolites and RNA to and from the core for RNA transcription during infection. It is possible that the synthetic core-like particles have an incomplete complement of VP7 spikes because the ratio of VP7 to VP3 produced in the dual expression system is less than the 13:1 required for complete core-like particles. Only the VP7 spikes which have the strongest affinity for the VP3 inner core and are involved in maintaining the structural integrity of the core-like particle are incorporated. The BTV core-like particle shows greater morphological similarity to the rotavirus than to the reovirus core particle.

Preparation and neutron diffraction of superconducting “tetragonal” and non-superconducting orthorhombic Tl2Ba2Cu1O6

Abstract Many different samples of Tl 2 Ba 2 Cu 1 O 6 have been prepared by different heat treatments at relatively low temperature. The material as first prepared is clearly orthorhombic and non-superconducting, but on annealing and quenching, the samples become almost tetragonal with high T c . Various T c values between 3+ O 2- atoms are missing, creating the electron holes apparently necessary for superconductivity. The main difference between the various samples appears to be that the non-superconducting material is orthorhombic, with a well ordered superstructure, while the superconducting material is pseudo-tetragonal, with disordered oxygen within the TlO plane, as for the higher superconducting members of the Tl 2 Ca n Ba 2 Cu n +1 O 2( n +3 ) series. Superconductivity then appears to depend on the precise structural arrangement, and not just on stoichiometry and the number of electron holes.

Powder X-ray and neutron diffraction study of the superconductor Bi2Sr2CaCu2O8

A sample of the new BiO-perovskite superconductor has been synthesized. X-ray diffraction has been used to locate the cations while neutron diffraction has been used to determine the precise oxygen co-ordination. The stricture contains CuO 2 planes with Cu coordinated to four oxygens at 1.92A within the plane, plus more distant oxygen at 2.65A perpendicular to the plane. Two such copper oxide (perovskite) planes are intercalated with planes of BiO. The stricture is described in an Fmmm subcell (5.4A, 5.4A, 30.8A), except for the oxygen within the BiO layers, and to a lesser extent the Bi itself, which require a x5 larger b-axis. The X-ray refinement in Bbmm indicates that this Bi displacement is 0.27A.

A model for the superstructure of Bi2Sr2CaCu2O8.2

Abstract A model is proposed for the superstructure of Bi 2 Sr 2 CaCu 2 O 8.2 . It involves the addition of one in ten oxygen atoms in the BiO planes and a displacement of the surrounding atoms. This model is consistent with electron microscope, neutron and X-ray diffraction data. In particular it is consistent with the symmetry determined by convergent beam electron diffraction and with details of the high resolution electron microscope image contrast.

The concerted conformational changes during human rhinovirus 2 uncoating.

Delivery of the rhinovirus genome into the cytoplasm involves a cooperative structural modification of the viral capsid. We have studied this phenomenon for human rhinovirus serotype 2 (HRV2). The structure of the empty capsid has been determined to a resolution of better than 15 A by cryo-electron microscopy, and the atomic structure of native HRV2 was used to examine conformational changes of the capsid. The two proteins around the 5-fold axes make an iris type of movement to open a 10 A diameter channel which allows the RNA genome to exit, and the N terminus of VP1 exits the capsid at the pseudo 3-fold axis. A remarkable modification occurs at the 2-fold axes where the N-terminal loop of VP2 bends inward, probably to detach the RNA.

Adenovirus 3 penton dodecahedron exhibits structural changes of the base on fibre binding.

It was recently shown that co‐expression of adenovirus type 3 (Ad3) penton base and fibre in the baculovirus system produces dodecahedral particles, as does the expression of the penton base alone. The structure of both of these dodecahedral particles, with and without fibre, has been determined by cryoelectron microscopy and 3‐dimensional reconstruction techniques to a resolution of 25 and 20 A, respectively. The general form of the penton base resembles that of the base protein in the recent reconstruction of adenovirus type 2. There is a remarkable difference in the penton base structure with and without the fibre. The five small protuberances on the outer surface of each base move away from the 5‐fold axis by approximately 15 A when the fibre is present. These protuberances are of relatively low density and most probably represent a flexible loop possibly containing the RGD site involved in integrin binding. The fibre is apparently bound to the outer surface of the penton base, rather than inserted into it. The fibre is flexible and the shaft contains two distinct globular regions 26 A in diameter. The volume of the inner cavity of the dodecahedron is 350 +/− 100 nm3. This small volume precludes the use of the inner cavity to house genetic information for gene therapy; however, the possibility remains of linking the gene to the dodecahedron surface in the hope that it will be internalized with the dodecahedron.