Recently in PX Category

The facilities and staff at the SIBYLS beamline contributed to this recent structural study of a human antibody that is able to neutralize Marburg and Ebola viruses.

eos_cell_marburg.jpg

The filoviruses, including Marburg and Ebola, express a single glycoprotein on their surface, termed GP, which is responsible for attachment and entry of target cells. Filovirus GPs differ by up to 70% in protein sequence, and no antibodies are yet described that cross-react among them. Here, we present the 3.6 Å crystal structure of Marburg virus GP in complex with a cross-reactive antibody from a human survivor, and a lower resolution structure of the antibody bound to Ebola virus GP. The antibody, MR78, recognizes a GP1 epitope conserved across the filovirus family, which likely represents the binding site of their NPC1 receptor. Indeed, MR78 blocks binding of the essential NPC1 domain C. These structures and additional small-angle X-ray scattering of mucin-containing MARV and EBOV GPs suggest why such antibodies were not previously elicited in studies of Ebola virus, and provide critical templates for development of immunotherapeutics and inhibitors of entry.

Hashiguchi T, Fusco ML, Bornholdt ZA, Lee JE, Flyak AI, Matsuoka R, Kohda D, Yanagi Y, Hammel M, Crowe JE, Saphire EO. “Structural basis for marburg virus neutralization by a cross-reactive human antibody.” Cell 2015 Feb 26 ;160(5):904-12 link

Keeping DOMO happy

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Hello DOMO users,

DOMO is fairly robust, and is capable of handling your precious crystals mounted in a variety of bases:

pin-types.jpg

However, you must take some care when gluing or epoxying the pins into the bases. If there is too much glue or epoxy or you inadvertantly get some on the sides or bottom of the base this will cause the robot to jam, which will require time-wasting reset procedures, lost samples, and unhappy beamline support personnel.

Here is a recent example of several pins where the user (who will remain unnamed) applied entirely too much epoxy. Somehow the user was able to load these pins into the cassette, but they caused the robot to jam.

bad_pins_for_DOMO.jpg

There are more detailed tips and hints on the SSRL SMB website for preparing your bases and pins.

Researchers from Scripps Research Institute and the University of Glasgow have published a detailed molecular model of how UVR8, a unique heme-free plant photoreceptor, senses UV-B light via an intricate interacting mesh of Tryptophan residues positioned at the UVR8 dimer interface which ultimately results in the disruption of a salt bridge and dissociation of the UVR8 dimer.

uvr8_science_highlight.jpg

The recently identified plant photoreceptor UVR8 triggers regulatory changes in gene expression in response to ultraviolet-B (UV-B) light via an unknown mechanism. Here, crystallographic and solution structures of the UVR8 homodimer, together with mutagenesis and far-UV circular dichroism spectroscopy, reveal its mechanisms for UV-B perception and signal transduction. β-propeller subunits form a remarkable, tryptophan-dominated, dimer interface stitched together by a complex salt-bridge network. Salt-bridging arginines flank the excitonically coupled cross-dimer tryptophan “pyramid” responsible for UV-B sensing. Photoreception reversibly disrupts salt bridges, triggering dimer dissociation and signal initiation. Mutation of a single tryptophan to phenylalanine retunes the photoreceptor to detect UV-C wavelengths. Our analyses establish how UVR8 functions as a photoreceptor without a prosthetic chromophore to promote plant development and survival in sunlight.

Christie, J. M., Arvai, A. S., Baxter, K. J., Heilmann, M., Pratt, A. J., O’Hara, A., Kelly, S. M., Hothorn, M., Smith, B. O., Hitomi, K., Jenkins, G. I., Getzoff, D. G.”Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges” Science. Published Online February 9 2012

Members of the Noller lab recently published a 3.3 Å resolution structure of a complex containing the ribosomal release factor (RF3) locked in its GTP-bound state (mimicked using GDPNP) in association with the E. coli 70s ribosome. Crystallographic data for this project was collected at the SIBYLS beamline MX station.

The class II release factor RF3 is a GTPase related to elongation factor EF-G, which catalyzes release of class I release factors RF1 and RF2 from the ribosome after termination of protein synthesis. The 3.3 Å crystal structure of the RF3·GDPNP·ribosome complex provides a high-resolution description of interactions and structural rearrangements that occur when binding of this translational GTPase induces large-scale rotational movements in the ribosome. RF3 induces a 7° rotation of the body and 14° rotation of the head of the 30S ribosomal subunit, and itself undergoes inter- and intradomain conformational rearrangements. We suggest that ordering of critical elements of switch loop I and the P loop, which help to form the GTPase catalytic site, are caused by interactions between the G domain of RF3 and the sarcin-ricin loop of 23S rRNA. The rotational movements in the ribosome induced by RF3, and its distinctly different binding orientation to the sarcin-ricin loop of 23S rRNA, raise interesting implications for the mechanism of action of EF-G in translocation.


jie_ribosome.jpg

Zhou, J., Lancaster, L., Trakhanov, S., & Noller, H. F. “Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome.” RNA (New York, NY), 18(2), 230-240.

To free up space on the primary /data volume we’ve recently created compressed read-only archival filesystems (using the squashfs filesystem if you’re interested) for all MX and SAXS data collected at the SIBYLS beamline between 2007 and 2009. You will find the archives mounted as /2007_data, /2008_data, and /2009_data on most of the beamline computers. The MX ADSC *.img files which take up the bulk of the space have been moved from /data to the archival volumes, but the SAXS *.mccd files have only been copied to the archival system.

For the MX endstation we've characterized the dependence of the direct beam on detector distance and 2-theta. We collected 4 sweeps of the detector from 120mm to 1600mm combined with 2-theta offsets from 0º up to 12º. These are the gnuplot 3D plots of the data.
xbeams.png ybeams.png
This set of 3D plots uses gnuplots pm3d settings to generate colorful versions:
xbeam3ds.png ybeam3ds.png
Click the images to view larger versions, and hit the "jump" to read the gory details of the polynomial equation used to determine x-beam and y-beam given any value of detector distance (CCD_Z) and 2-theta.
Wen Zhang and Jack Dunkle in the Cate lab have a nice report out in the August 21, 2009 issue of Science describing their latest crystal structures of the E. coli ribosome with and without tRNA mimcs. These new structure shed light on the rachet-like action of the intact ribosome as it interacts with tRNA in the A, P, and E sites.

Zhang_Dunkle_Cate_Science.jpegAbstract:
Protein biosynthesis on the ribosome requires repeated cycles of ratcheting, which couples rotation of the two ribosomal subunits with respect to each other, and swiveling of the head domain of the small subunit. However, the molecular basis for how the two ribosomal subunits rearrange contacts with each other during ratcheting while remaining stably associated is not known. Here, we describe x-ray crystal structures of the intact Escherichia coli ribosome, either in the apo-form (3.5 angstrom resolution) or with one (4.0 angstrom resolution) or two (4.0 angstrom resolution) anticodon stem-loop tRNA mimics bound, that reveal intermediate states of intersubunit rotation. In the structures, the interface between the small and large ribosomal subunits rearranges in discrete steps along the ratcheting pathway. Positioning of the head domain of the small subunit is controlled by interactions with the large subunit and with the tRNA bound in the peptidyl-tRNA site. The intermediates observed here provide insight into how tRNAs move into the hybrid state of binding that precedes the final steps of mRNA and tRNA translocation.

Zhang W, Dunkle JA, Cate JHD. "Structures of the Ribosome in Intermediate States of Ratcheting" Science 21 August 2009: Vol. 325. no. 5943, pp. 1014 - 1017.
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