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Large Macromolecular Complexes in the Protein Data Bank: A Status Report

Shuchismita Dutta, Helen M. Berman
2005 Structure  
field of structural biology. The growing number of NMR and EM depositions to the PDB (Berman et al., 2000) The Research Collaboratory for Structural Bioinformatics Protein Data Bank has necessitated an evolution in the representation, archiving, and analysis of structural data. Along with the increase in the overall number of structures deposited to the PDB, the complexity of Piscataway, New Jersey 08854 these structures has also increased. For example, in the 1970s there were no more than two
more » ... hains in the The growing number of large macromolecular comcrystal asymmetric unit, whereas now there are strucplexes in the Protein Data Bank (PDB) has warranted tures with more than 10 different chains (Figure 2). If a closer look at these structures. An overview of the we measure complexity as a function of the number of types of molecules that form these large complexes chains in the biologically functional unit, the picture is is presented here. Some of the challenges at the PDB slightly different. Whereas in the 1970s the biological in representing, archiving, visualizing, and analyzing units of typical structures contained between one and these structures are discussed along with possible four chains, some of the structures deposited today, means to overcome them. like viruses and ribosomes, have far more complex biological assemblies. The number of chains is one measure of the size and complexity of a PDB entry; molecu-Introduction lar weight is another measure of the same. For the present discussion, biologically functional units with The Protein Data Bank (PDB) was established in 1971 greater that 500,000 Da are classified as large macro-(Bernstein et al., 1977) as an archive for biological macmolecular complexes. Since all of these structures have romolecular structures. By 1974 there were 12 protein multiple chains in the biological assembly, they represtructures in the archive, including myoglobin, hemosent both large and complex structures. Here we preglobin, carboxypeptidase A, and subtilisin (Table 1) . sent an overview of the types of molecules that are in-These structures are small, compact globular proteins cluded in this class and discuss key issues and that represent pioneering efforts by the founders of challenges that these large structures present to the macromolecular X-ray crystallography. Over time, the PDB with regard to their representation, archiving, visunumber of structures in the PDB has dramatically inalization, and analysis. creased (Figure 1 ) and at the time of this writing there are over 28,000 entries in the PDB archives. A number of advances in protein crystallography, the most popu-Overview and Biological Significance lar method of structure determination for biological macromolecules, have contributed significantly to this Although the large macromolecular complex structures represent a small portion of the PDB, it is important to growth. Recombinant DNA methods have made it possible to clone, express, and purify large quantities of note that the number of structures in this class is rapidly growing. Presently, there are a little over 430 nearly any biological macromolecule (protein or nucleic acid). Rapid and increasingly automated methods for entries (representing about 1.5% of the PDB holdings) that fit this classification, most of which were deposited crystallization have emerged. Synchrotrons provide intense sources of X-rays, while new detectors allow within the last ten years. While the majority of these large complexes were solved using X-ray crystallogra-rapid data collection. Finally, new and more automated software for crystal structure determinations as well as phy, almost 21% of this subset were derived either using electron microscopy, electron tomography, or relatively easy access to high-speed computing have also vastly reduced the time for data processing and electron diffraction. With a growing interest in solving structures of larger and larger complexes and with con-analysis. In addition to advances in macromolecular crystal-tinuing advances in the field, the proportion of large macromolecular structures in the PDB solved by EM is lography, new methods of structure determination have also contributed to the growth in PDB holdings. Struc-likely to increase. A survey of the large macromolecular complexes revealed that this class is currently com-tures determined using nuclear magnetic resonance (NMR) spectroscopy now represent about 15% of posed of some well-known assemblies, such as ribosomes and viruses, as well as multienzyme complexes PDB's holdings. Electron microscopy (EM) is being used to determine structures of very large complex and structural proteins. A list of the major types of complexes and assemblies comprising the large macromo-systems. Since the information obtained from these methods shed light on different aspects of the struc-lecular structures is shown in Table 2 . It is evident from this table that viruses comprise the largest group, fol-ture, stability, and function of biological macromolecules, each method has carved out its own niche in the lowed by ribosome and ribosomal complexes, large enzyme complexes, chaperonins, and structural protein assemblies.
doi:10.1016/j.str.2005.01.008 pmid:15766539 fatcat:4ejbd6yve5cp7keeptmpneh7fu

The Protein Data Bank and Its Uses in Structural Biology Education

Judith Voet, Shuchismita Dutta
2004 Journal of Biochemistry Education  
The Protein Data Bank (PDB) is a repository for the structures of proteins and nucleic acids. Itcontains les of their 3-dimensional coordinates, information on how these structures were determinedand references to the journal articles describing them. The PDB was established in 1971 by HelenBerman (it s present director) and has grown exponentially so that it now contains 25,000 data lesrepresenting X-ray crystallographic, NMR and other structure determinations. Database queryingand data
more » ... ools and resources at the PDB make it possible to search, compare and infer orpredict the function of newly identied proteins. Computer graphics capabilities make it possible foranyone to easily visualize and study the structural data. The capability to present beautiful graphicrepresentations of the 3-dimesnional structures of proteins and nucleic acids has been a boon to theeducation community. Communicating an understanding of these structures and the chemical forcesdetermining them and their interactions is one of the major aims of biochemistry and molecular biologyeducation. The ability to teach these principles visually has made a great dierence in our abilityto excite our students and provide them with physical interpretations for some abstract concepts inbiochemistry and molecular biology. In this talk we will explore some of the ways that the education community uses the PDB.
doi:10.16923/reb.v2i2.153 fatcat:ncgwikfnhbbxtehpz64tbiovey

Representation of viruses in the remediated PDB archive

Catherine L. Lawson, Shuchismita Dutta, John D. Westbrook, Kim Henrick, Helen M. Berman
2008 Acta Crystallographica Section D: Biological Crystallography  
Structures of such quaternary complexes or assemblies present many challenges for archival representation and validation, graphical display and analysis (Dutta & Berman, 2005) .  ... 
doi:10.1107/s0907444908017393 pmid:18645236 pmcid:PMC2677383 fatcat:jw6vevz23nghdmc4i66634yqje

Molecular storytelling for structural biology outreach and education

David Goodsell, Shuchismita Dutta, Maria Voigt, Christine Zardecki, Stephen Burley
2020 Acta Crystallographica Section A: Foundations and Advances  
Knowledge about the structure and function of biomolecules continues to grow exponentially, enabling us to "see" structural snapshots of biomolecular interactions and functional assemblies. At PDB-101, the educational portal of the RCSB Protein Data Bank, we have taken a storytelling approach to make this body of knowledge accessible and comprehensible to a wide community of students, educators and the general public. For 20 years, the Molecule of the Month series has utilized a traditional
more » ... strated storytelling approach that is regularly adapted for classroom instruction. Similar visual and interactive storytelling approaches are used to present topical subjects at PDB-101, and full curricular materials for building a detailed narrative around topics of particular interest. This emphasis on storytelling led to the Video Challenge for High School students, now in its 7th year. In this workshop, I will present some of the lessons we have learned for teaching and communicating structural biology using the PDB archive of biomolecular structures. PDB-101 and the RCSB PDB are funded by the National Science Foundation
doi:10.1107/s0108767320099900 fatcat:ueybdthjd5fetd4yjfdn4ow5xe

The Crystal Structure of Drosophila NLP-Core Provides Insight into Pentamer Formation and Histone Binding

V.M.Haridasan Namboodiri, Shuchismita Dutta, Ildikó V Akey, James F Head, Christopher W Akey
2003 Structure  
Dutta, S., Akey, I.V., Dingwall, C., Hartman, K.L., Laue, T., Nolte, Thermal stability assays were carried out on the purified proteins R.T., Head, J.F., and Akey, C.W. (2001).  ... 
doi:10.1016/s0969-2126(03)00007-8 pmid:12575937 fatcat:4el7kmiswzdafbr2jzezeqzqae

The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology

David S. Goodsell, Shuchismita Dutta, Christine Zardecki, Maria Voigt, Helen M. Berman, Stephen K. Burley
2015 PLoS Biology  
The Research Collaboratory for Structural Bioinformatics (RCSB) Molecule of the Month series provides a curated introduction to the 3-D biomolecular structures available in the Protein Data Bank archive and the tools that are available at the RCSB website for accessing and exploring them. A variety of educational materials, such as articles, videos, posters, hands-on activities, lesson plans, and curricula, build on this series for use in a variety of educational settings as a general
more » ... on to key topics, such as enzyme action, protein synthesis, and viruses. The series and associated educational materials are freely available at www.rcsb.org.
doi:10.1371/journal.pbio.1002140 pmid:25942442 pmcid:PMC4420264 fatcat:mq3g6lso4jcpvlvc6empbdfkwi

Trendspotting in the Protein Data Bank

Helen M. Berman, Buvaneswari Coimbatore Narayanan, Luigi Di Costanzo, Shuchismita Dutta, Sutapa Ghosh, Brian P. Hudson, Catherine L. Lawson, Ezra Peisach, Andreas Prlić, Peter W. Rose, Chenghua Shao, Huanwang Yang (+2 others)
2013 FEBS Letters  
The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85 000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever-growing amount of PDB data.
doi:10.1016/j.febslet.2012.12.029 pmid:23337870 pmcid:PMC4068610 fatcat:pc6muagsrzh6lcqjm4ewkct5sa

The next generation RCSB.org

Justin Flatt, Jose M. Duarte, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Shuchismita Dutta, Robert Lowe, Alexander S. Rose, Yana Rose, Joan Segura, John Westbrook (+1 others)
2021 Acta Crystallographica Section A: Foundations and Advances  
doi:10.1107/s0108767321097245 fatcat:a4cblmwfejdfvmtsdxkcvhnwve

Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences

Shuchismita Dutta, Christine Zardecki, David S. Goodsell, Helen M. Berman
2010 Journal of Applied Crystallography  
Cryst. (2010). 43, 1224-1229 Shuchismita Dutta et al. RCSB PDB resources 1227 Dutta et al. RCSB PDB resources J. Appl.  ...  Cryst. (2010). 43, 1224-1229 1229 Figure 1 12291 Dutta et al. RCSB PDB resources J. Appl.  ... 
doi:10.1107/s002188981002371x pmid:20877496 pmcid:PMC2943739 fatcat:tumibltfefcxzomabkgef2vkmq

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank

Shuchismita Dutta, Dimitris Dimitropoulos, Zukang Feng, Irina Persikova, Sanchayita Sen, Chenghua Shao, John Westbrook, Jasmine Young, Marina A. Zhuravleva, Gerard J. Kleywegt, Helen M. Berman
2014 Biopolymers  
The peptide-like inhibitors in 370 PDB entries also 660 Dutta et al. contain at least two consecutive peptide bonds.  ...  The linker between the two molecules is succinic acid (SIN). 662 Dutta et al. representation was also used for peptide-like molecules in which the directionality of the peptide linkages is not exclusively  ... 
doi:10.1002/bip.22434 pmid:24173824 pmcid:PMC3992913 fatcat:fsy4z23qcfgnvjj2jpn3stgwta

New online curriculum: the PDB pipeline and data archiving

Catherine L. Lawson, Margaret J. Gabanyi, John Westbrook, Jasmine Young, Shuchismita Dutta, Ezra Peisach, Brian P. Hudson, Peter Rose, Jose Duarte, Amy Sarjeant, Stephen K. Burley, Helen M. Berman
2018 Acta Crystallographica Section A: Foundations and Advances  
doi:10.1107/s0108767318097568 fatcat:vksyzw665jee3hu52qwgllh2sq

Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank

Huanwang Yang, Vladimir Guranovic, Shuchismita Dutta, Zukang Feng, Helen M. Berman, John D. Westbrook
2004 Acta Crystallographica Section D: Biological Crystallography  
The RCSB Protein Data Bank (PDB) has a number of options for deposition of structural data and has developed software tools to facilitate the process. In addition to ADIT and the PDB Validation Suite, a new software application, pdb_extract, has been designed to promote automatic data deposition of structures solved by X-ray diffraction. The pdb_extract software can extract information about data reduction, phasing, molecular replacement, density modi®cation and re®nement from the output ®les
more » ... oduced by many X-ray crystallographic applications. The options, procedures and tools for accurate and automated PDB data deposition are described here.
doi:10.1107/s0907444904019419 pmid:15388930 fatcat:uuhfm7tfu5auljt24aifx3bd6e

The RCSB Protein Data Bank: new resources for research and education

Peter W. Rose, Chunxiao Bi, Wolfgang F. Bluhm, Cole H. Christie, Dimitris Dimitropoulos, Shuchismita Dutta, Rachel K. Green, David S. Goodsell, Andreas Prlić, Martha Quesada, Gregory B. Quinn, Alexander G. Ramos (+5 others)
2012 Nucleic Acids Research  
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical
more » ... ponent data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher's PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.
doi:10.1093/nar/gks1200 pmid:23193259 pmcid:PMC3531086 fatcat:jx4ewohcyrayre6yw4zmlqu74q

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

Peter W. Rose, Andreas Prlić, Chunxiao Bi, Wolfgang F. Bluhm, Cole H. Christie, Shuchismita Dutta, Rachel Kramer Green, David S. Goodsell, John D. Westbrook, Jesse Woo, Jasmine Young, Christine Zardecki (+3 others)
2014 Nucleic Acids Research  
The RCSB Protein Data Bank (RCSB PDB, http: //www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external
more » ... ical resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.
doi:10.1093/nar/gku1214 pmid:25428375 pmcid:PMC4383988 fatcat:ms62oq4lnbep5i7dq2qp4f3hwm

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh (+28 others)
2018 Nucleic Acids Research  
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular
more » ... llography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a 'Structural View of Biology.'
doi:10.1093/nar/gky1004 pmid:30357411 pmcid:PMC6324064 fatcat:clctmqo6ujaifm7s27vk3s2h7i
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