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For answers to questions ranging from "how can I deposit my structure" to "how can I create a report about the structures I've found" to "what is DNA?", the RCSB PDB actively maintains several e-mail help desks. Responses are rapidly returned.
MEETINGS, EXHIBITS, AND WORKSHOPS
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Art of Science Exhibit at Texas A&M and Rutgers
The RCSB PDB's "Art of Science" exhibit was on tour this
past spring. It appeared at Texas A&M University's Visual
Arts Gallery in the Memorial Student Center (April 13 - May 15,
2005). The show was also part of the American Chemical Society
Mid-Atlantic Regional Meeting (MARM) held at Rutgers (May 22-25,
2005).
The Art of Science traveling exhibit looks at the beauty inherent
in protein structures. It displays images of molecules in the
PDB, including the pictures available from Structure Explorer
pages and from Molecule of the Month features. Since its
beginnings at a space dedicated to art exhibits at Rutgers
University, the show has traveled to many places, including
EMBL-Hamburg, Germany; University of Wisconsin-Madison; California
State University, Fullerton; Purdue University; and Hyderabad,
India. The RCSB PDB would like to see the "Art of
Science" travel to other places. If you would be interested
in sponsoring this exhibit at your institution, please let us know
at info@rcsb.org.
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RCSB PDB Educational Resources Poster
Resources for education available from the RCSB PDB are
highlighted on a poster that is available for download (www.rcsb.org/pdb/education.html; 8 1/2 by 11 inches).
- The Molecule of the Month feature illustrates important biological molecules and how they function through descriptive text, pictures, and links to specific PDB entries and other resources.
- The RCSB PDB Newsletter regularly features interviews with members of the community and descriptions of how the PDB is used in all levels of education.
- The Education Page provides resources for learning about Proteins and Nucleic Acids, protein documentaries, and suggested reading materials and links.
- RCSB PDB tools for finding and visualizing proteins are used in the classroom in a variety of ways, including downloading molecular images, exploring the links to information found in journals, and trying different keyword queries to locate specific proteins.
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RCSB Meetings: ACA and ISMB
Highlights from the Annual Meeting of the American
Crystallographic Association (ACA) held May 28 - June 2, 2005 in
Orlando, FL included exhibiting in "Data Alley", along
with CCP4 and CCDC. RCSB PDB staff were on hand to answer
questions and provide demonstrations of deposition software and
the beta site. Annotator Kyle Burkhardt presented a tutorial on
using RCSB PDB validation software at the "Workshop on
Macromolecular Structure Validation."
The RCSB PDB also exhibited at the 13th Annual Meeting of the
International Society for Computational Biology ("Intelligent
Systems for Molecular Biology" June 25 - 29 in Detroit,
Michigan). Wolfgang Bluhm presented "Structural
Bioinformatics Education from the RCSB Protein Data Bank" as
part the Education session.
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RCSB Poster Prize awarded at RECOMB and ACA
Thanks to the students and judges who participated in the
recent RCSB PDB Poster awards. Details are available at www.rcsb.org/pdb/poster_prize.html. The next
award will be presented at the XX Congress of the International
Union of Crystallography (August 23-31 2005 in Florence,
Italy).
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At the Ninth Annual International Conference on Research in
Computational Molecular Biology (RECOMB, May 14-18, Cambridge,
MA), the RECOMB & PDB Poster Awards recognizing insight and
innovation in structural computational biology went to
"Comparative Modeling of Mainly-Beta Proteins by Profile
Wrapping" by Andrew V. McDonnell, Matthew Menke, Nathan
Palmer, Jonathan King, Lenore Cowen, Bonnie Berger (MIT) and
"MAPPIS: Multiple Alignment of Protein-Protein
Interfaces" by Alexandra Shulman-Peleg, Maxim Shatsky, Ruth
Nussinov and Haim J. Wolfson (Tel-Aviv University).
- At the ACA, the award for best student presentation went to
"Safety in Cycling: Novel Redox Proteins from Escherichia
coli" by Melanie A. Adams (pictured) and Zongchao Jia
(Queen's University).
Molecules of the Quarter
The
Molecule of the Month series explores the functions and significance
of selected biological macromolecules for a general audience.
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April: Kinesin
Kinesins are used for many tasks in cells. Typical cells
contain an array of microtubules, all pointed from the center of
the cell outwards to the surface. Kinesins are used to drag
large objects, like lysozomes or endoplasmic reticulum, outwards
away from the nucleus and towards the surface. Dyneins are used
for the opposite function, to pull things inwards. Kinesins drag
materials down the enormous length of nerve axons--this function
is how kinesins were discovered. Kinesins are also used to slide
microtubules next to one another, for instance, during the
process of creating two separate systems of microtubules to
separate chromosomes when the cell divides.
 PDB ID 3kin: Kozielski, F., Sack, S., Marx, A., Thormahlen, M., Schonbrunn, E., Biou, V., Thompson, A., Mandelkow, E. M., Mandelkow, E.: The crystal structure of dimeric kinesin and implications for microtubule-dependent motility. Cell 91 pp. 985 (1997)
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May: Self-splicing RNA.
In plants and animals, most RNA molecules are made as long
precursors that need to be trimmed and reassembled to create the
final active molecule. These precursor RNA molecules are
composed of exons, which are the important parts, separated by
introns, which must be removed. In most cases, the RNA is cut
and spliced together by a spliceosome, a molecular machine
composed of protein and RNA. In a few cases, however, the RNA
can perform the splicing reaction on its own. The first example,
discovered by Thomas Cech, was a ribosomal RNA found in a
protozoan. Since then, hundreds of examples have been identified
in genome sequences of many organisms. The example shown here,
from PDB entry 1u6b, is part of a bacterial transfer RNA that
must be spliced before it can adopt its functional form. In the
illustration, the large structure in green is the intron, which
uses a GTP and two magnesium ions to remove itself. The two
exons that will be spliced together are colored red and
blue--note that only a small piece of each exon is included in
the structure.
PDB ID 1u6b: Adams, P. L., Stahley, M. R.,
Kosek, A. B., Wang, J., Strobel, S. A.: Crystal Structure of a
Self-Splicing Group I Intron with Both Exons. Nature 430 pp. 45
(2004)
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June: Carotenoid Oxygenase
The bright color of carrots and many other orange and yellow
vegetables is caused by carotenoid molecules such as
beta-carotene. Carotenoids are long, thin molecules with a
string of carbon-carbon double bonds in a row. These bonds
absorb light and give carotenoids their characteristic yellow
color. Hundreds of different types have been discovered in
different plants, where they color flowers, leaves, fruits, and
even the roots. Carotenoids are remarkably useful, both for the
plant and for the people eating the plant. In plants,
carotenoids assist the chlorophyll molecules that absorb light
in photosynthesis. Carotenoids also absorb excess light when it
reaches dangerous levels. Our retinas contain carotenoids such
as lutein that protect us from excess light that might damage
our eyes. Carotenoids also are antioxidants that scavenge
reactive forms of oxygen, destroying them before they damage our
molecular machinery.
 PDB ID 2biw. Kloer, D. P., Ruch, S., Al-Babili, S., Beyer, P., Schulz, G. E.: The Structure of a Retinal-Forming Carotenoid Oxygenase Science 308 pp. 267 (2005)
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