25 research outputs found
The exosome‐binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase
Clamp loader ATPases and the evolution of DNA replication machinery
Clamp loaders are pentameric ATPases of the AAA+ family that operate to ensure processive DNA replication. They do so by loading onto DNA the ring-shaped sliding clamps that tether the polymerase to the DNA. Structural and biochemical analysis of clamp loaders has shown how, despite differences in composition across different branches of life, all clamp loaders undergo the same concerted conformational transformations, which generate a binding surface for the open clamp and an internal spiral chamber into which the DNA at the replication fork can slide, triggering ATP hydrolysis, release of the clamp loader, and closure of the clamp round the DNA. We review here the current understanding of the clamp loader mechanism and discuss the implications of the differences between clamp loaders from the different branches of life
Preliminary analysis of crystals of panicum mosaic virus (PMV) by X-ray diffraction and atomic force microscopy.
The crystallographic structure of Panicum Mosaic Virus (PMV).
The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7Å, b=403.9Å and c=412.5Å, with β=89.7°. The asymmetric unit was two entire T=3 virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacco Necrosis Virus (TNV), of ∼20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The virus has Ca(++) ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1-53, 1-49 and 1-21 of the A, B and C subunits, respectively, and the four C-terminal residues (239-242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent "arm" that intertwines with symmetry equivalent "arms" at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A-B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other viruses
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Preliminary analysis of crystals of panicum mosaic virus (PMV) by X-ray diffraction and atomic force microscopy.
Panicum mosaic virus (PMV), a spherical virus of diameter about 300 A, has been crystallized in a form suitable for high-resolution structural analysis. The crystals were grown from 15% PEG 400 at room temperature and could be flash-frozen directly from their mother liquor. The crystals diffracted to beyond 2.7 A resolution. A data set was collected at 100 K to an effective resolution of 3.2 A [Weiss (2001), J. Appl. Cryst. 34, 130-135]. The crystals belonged to space group P2(1), with unit-cell parameters a=411.7, b=403.9, c=412.5 A, beta=89.7 degrees . Self-rotation functions and molecular replacement with tobacco necrosis virus as the probe model yielded tentative positions and orientations for the two entire virus particles comprising the asymmetric unit and implied a pseudo-face-centered cubic packing arrangement. Investigation of lightly glutaraldehyde-fixed crystals in water using atomic force microscopy confirms the packing arrangement given by the molecular-replacement result. The images also show that contaminating virions of the satellite virus to PMV, known as satellite panicum mosaic virus (SPMV), can be incorporated into the PMV crystals by insertion into the interstices between PMV virions in the lattice. This is the first observation of such a phenomenon in macromolecular crystals
Four crystal forms of a Bence-Jones protein
Four crystal forms have been grown and characterized by X-ray diffraction of a Bence-Jones protein collected from the urine of a multiple myeloma patient more than 40 y ago. The trigonal crystal form may shed some light on the formation of fibrils common to certain storage diseases
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Four crystal forms of a Bence-Jones protein.
Four crystal forms have been grown and characterized by X-ray diffraction of a Bence-Jones protein collected from the urine of a multiple myeloma patient more than 40 years ago. Closely related tetragonal and orthorhombic forms belonging to space groups P4(3)2(1)2 and P2(1)2(1)2(1), with unit-cell parameters a = b = 68.7, c = 182.1 and a = 67.7, b = 69.4, c = 87.3 A, diffract to 1.5 and 1.9 A, respectively. Two closely related trigonal forms, both belonging to space group P3(1)21 with unit-cell parameters a = b = 154.3 A but differing by a doubling of the c axis, one 46.9 A and the other 94.0 A, diffract to 2.9 and 2.6 A resolution, respectively. The trigonal crystal of short c-axis length shows a positive indication of twinning. The trigonal crystal of longer c axis, which appeared only after eight months of incubation at room temperature, is likely to be composed of proteolytically degraded molecules and unlike the other crystal forms contains two entire Bence-Jones dimers in the asymmetric unit. This latter crystal form may shed some light on the formation of fibrils common to certain storage diseases