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We determined the structure of the mammalian Cyt.c-CcO complex and identified the electron transfer pathway from Cyt.c to Cu SB A sb of CcO ([20]) PDB ID: 5IY5). A proton is then transferred from the proton pool to the P-side of CcO via the hydrogen-bond network upon electron transfer at each step of the reaction step from the P- to F-, F- to O-, O- to E- and E- to R-states. I started on crystallographic studies of cytochrome c (Cyt.c) in the later 1960s at the Institute for Protein Research, Osaka University. We determined the structure of the mammalian Cyt.c-CcO complex at 2.0 Å resolution and identified the "soft and specific" interaction between Cyt.c and CcO, which affected high-efficiency inter-molecular electron transfer. [Extracted from the article]

The X-ray structure of a [2Fe-2S]-type ferredoxin (Fd) from Spirulina platensis , solved by a collaborative group led by Profs Masao Kakudo, Yukiteru Katsube and Hiroshi Matsubara, was the first high-resolution structure of a plant-type Fd deposited in the Protein Data Bank. The main chain structure, comprising a [2Fe-2S] cluster ligated by four conserved cysteine residues, together with a molecular evolutionary study based on a series of amino acid sequence determinations, was reported in Nature in 1980. The consequent detailed crystallographic analysis, including crystallization, heavy atom derivatization, data collection, phase calculation and model building, was published by the same group in the Journal of Biochemistry in 1981. The pioneering X-ray analysis of S. platensis Fd at 2.5 Å resolution was a key milestone in structural research on the photosynthetic electron transport chain, informing related and challenging studies on other components of the photosynthetic electron transfer chain. [ABSTRACT FROM AUTHOR]

The capsid structures of particles of Rice dwarf virus that consisted of different components, namely, intact particles, empty particles lacking the 12 segments of double-stranded RNA (dsRNA), and virus-like particles composed of only the P3 core and P8 outer capsid proteins, generated with a baculovirus gene-expression system, were determined by cryo-electron microscopy. Combining the results with those of biochemical analysis, we assigned proteins of the transcriptional machinery and dsRNA to density clusters around the 5-fold axes and along the radial concentric layers, respectively. P7 protein, a component of the transcriptional machinery, was assigned to the outermost region of the density clusters. The density connecting the transcription complex to the outermost RNA densities implied interactions between the dsRNA and the P7 protein. Our structural analysis and the non-specific nucleic acid-binding activity of P7 explain the spiral organization of dsRNA around the 5-fold axis. [ABSTRACT FROM PUBLISHER]

In order to elucidate the mechanism of the thermostability of proteins from hyperthermophiles, X-ray crystalline structures of pyrrolidone carboxyl peptidase from a hyper-thermophile, Pyrococcus furiosus (PfPCP), and its mutant protein with Ser substituted at Cys142 and Cys188 were determined at 2.2 and 2.7 Å resolution, respectively. The obtained structures were compared with those previously reported for pyrrolidone car-boxyl peptidases from a hyperthermophilie, Thermococcus litoralis (TlPCP), and from a mesophile, Bacillus amyloliquefaciens (BaPCP). The PfPCP structure is a tetramer of four identical subunits similar to that of the TlPCP and BaPCP. The largest structural changes among the three PCPs were detected in the C-terminal protrusion, which interacts with that of another subunit. A comparison of the three structures indicated that the high stability of PfPCP is caused by increases in hydrophobic interactions and hydrogen bonds, the formation of an intersubunit ion-pair network, and improvement to an ideal conformation. On the basis of the structures of the three proteins, it can be concluded that PfPCP does not have any special factors responsible for its extremely high stability and that the conformational structure of PfPCP is superior in its combination of positive and negative stabilizing factors compared with BaPCP. [ABSTRACT FROM AUTHOR]

The single-stranded DNA (ssDNA) binding protein from Escherichia coli CEcoSSB) plays a central role in DNA replication, recombination, and repair. The tertiary structure of EcoSSB was determined at 2.2 Å resolution. This is rather higher resolution than previously reported. Crystals were grown from the homogeneous intact protein but the EcoSSB tetramer in the crystals contains truncated subunits lacking a part of the C-ter-minal. The structure determined includes biologically important flexible loops and C-terminal regions, and revealed the existence of concavities. These concavities include the residues important for ssDNA binding. An ssDNA can be fitted on the concavities and further stabilized through interactions with the loops forming flexible lids. It seems likely to play a central role in the binding of ssDNA [ABSTRACT FROM AUTHOR]

The overall and internal structures of the silkworm Bombyx mori cytoplasmic polyhedrosis virus was investigated by small-angle neutron scattering using the contrast variation method. Data were collected in aqueous buffer solutions containing 0, 50,75, and 100% D2O in the q range of 0.002 to 0.0774 Å–1at 5°C. The radius of gyration at infinite contrast was estimated to be 336 Å. The contrast matching point of the virus was determined to correspond to about 50% D2O level, evidence that the virus is composed of protein and nucleic acid. The virus was basically spherical and had a diameter of about 700 Å. The main feature of its structure is the clustering of protein into two concentric shells separated by about 100 Å. Most of the RNA moieties are located in the central core and between these two protein shells. However, the distance distribution function P(r) showed a minor distribution beyond a distance of r=700 Å, with a maximum particle distance of the virus of 1350 Å. This is indicative of an external structure region with very low scattering density, in addition to the basic spherical structure. This external region is thought to correspond to twelve pyramidal protruding spikes shown by electron microscopic studies [ABSTRACT FROM AUTHOR]

The Crystal Structure of the 20S proteasome from bovine liver was determined by the molecular replacement method using the structure of the 20S proteasome from the yeast Saccharomyces cerevisiae. The initial phases were refined by density modification coupled with non-crystallographic symmetry averaging. The structural model was refined with the program CNS. The final R-factor and Rfree were 0.25 and 0.29, respectively. The constitutive proteasome without any contamination by the immunoproteasome was identified in the crystal structure. [ABSTRACT FROM AUTHOR]

20S proteasomes from higher eukaryotes have immunological functions rather than those from archibacteria or yeast. To clarify the mechanism of the sorting and production of antigen-presenting peptides, it is important and worthwhile to determine the structure of mammalian proteasomes using a third generation synchrotron radiation source. Here we report new crystal forms of 20S proteasomes from bovine liver and preliminary structure analysis of them. The crystals belong to the same space group but have different cell dimensions. One crystal (form I) belongs to space group P212121 with unit cell dimensions of a = 124.8, b = 197.4, c = 323.8 Å, and diffracts to 3.0 Å resolution. The other crystal (form II) belongs to the same space group with a = 115.1, b = 205.6, c = 316.0 Å, and diffracts to 4.0 Å resolution. The diffraction data for the form I crystal provided an interpretable electron density map for presenting the structural differences from yeast proteasomes. [ABSTRACT FROM AUTHOR]