Beginner’s Guide to PDB Structures and the PDBx/mmCIF Format
The constantly-growing PDB is a reflection of the research that is happening in laboratories across the world. This can make it both exciting and challenging to use the database in research and education.
What does PDBx mean? Where are all the hydrogen atoms in this file? Should I care about the R-factor? Why are there 20 overlapped structures in my file? These questions and many others are explored in PDB-101's Guide to Understanding PDB Data. This resource was created to help users navigate through the contents of the archive without having a detailed background in structural biology. Topics cover biological assemblies, molecular graphics programs, R-value and R-free, and more.
A Beginner’s Guide to PDB Structures and the PDBx/mmCIF Format has been added to this collection. The PDBx/mmCIF file format and data dictionary is the basis of wwPDB data deposition, annotation, and archiving of PDB data from all supported experimental methods. And as of July 1st 2019, submission of PDBx/mmCIF format files for crystallographic depositions to the PDB is mandatory.
Summer Newsletter Published
This issue highlights the Impact of PDB Structures on US FDA Drug Approvals; OneDep Improvements: Ligand Validation Images and Electron Density Maps; Award-winning videos; and more.
Create a Hemoglobin Bean Bag Toss
In 1962, Max Ferdinand Perutz and John Cowdery Kendrew received the Nobel Prize in Chemistry "for their studies of the structures of globular proteins."
HemoHole is a game where hemoglobin has holes where the heme bean-bags can be tossed through. It was created at Rutgers by Institute for Quantitative Biomedicine graduate students Kristin Blacklock, Elliott Dolan, Will Hansen, Nancy Hernandez, and Dmitri Zorine.
Learn About HIV and AIDS at PDB-101
The AIDS epidemic began a few decades ago and since then scientists have revealed the atomic structures of most of the molecules in HIV. Using these structures, researchers have designed new treatments for HIV infection, which are now part of effective drug regimens that halt the growth of the virus. Structures of HIV molecules also provide new hope for development of vaccines and methods to rid an infected individual of the latent virus.
New Flyer: Antibiotics in Action
Antibiotics allow us` to fight infections by pathogenic bacteria. They attack essential molecular machines in bacteria, stopping or slowing their action, ultimately slowing growth or killing the cell.
Annual Report Published
Download the 2018 Annual Report (PDF) for an overview of recent Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education activities.
This review highlights many RCSB PDB accomplishments, including a look at the global impact of the resource.
These bulletins provide a yearly snapshot of RCSB PDB activities and the state of the PDB archive. If you would like a printed copy, please send your postal address to email@example.com.
Award-Winning Videos on Antibiotic Resistance
The sixth edition of the Video Challenge for High School Students shows how high school students are excellent science communicators. Submitted videos demonstrate tremendous creativity, and used many storytelling approaches to communicate the Mechanisms of Bacterial Resistance to Aminoglycoside Antibiotics.
Our panel of expert judges (Disan Davis (RockEDU Science Outreach, The Rockefeller University), Ella Marushchenko (Ella Maru Studio, Inc.), and Andrew G. McArthur (McMaster University, and the Comprehensive Antibiotic Resistance Database (CARD)) scored the videos based on Quality of Storytelling (20%), Quality of Science Communication (30%), Quality of Public Health Message (10%), Originality and Creativity (20%), Quality of Production (10%), and Proper Accreditation (10%).
The general public voted for the Viewer's Choice Award.
- First Place: The Criminal Case of the Aminoglycoside Misuser by Brean Bognot and Cayla Tolentino of Mira Mesa High School, San Diego, CA (Team Advisor: Lisa Yoneda)
- Second Place: New Arms Race Aminoglycoside Antibiotics by Anvi Surapaneni and Vivian Hir of The Quarry Lane School, Dublin, CA (Team Advisor: Alina Hamm)
- Third Place: The Three Little Bacteria and the Big Bad Tobramycin by Carlos Hernandez, Jeff Huang, and Shamir Sheikh of Stuyvesant High School, New York, NY (Team Advisor: Gilbert Papagayo)
- Viewer's Choice: Mechanisms of Aminoglycoside Antibiotic Resistance by Charumathi Badrinath of Rye Country Day School, Rye, NY (Team Advisor: Jennifer Doran)
Many thanks to the expert judges, students, teachers, parents, and voters who made this exciting competition happen!
Education Corner: Exploring the Molecules of Biological Warfare in Virtual Reality
Other newsletter articles in this issue include a Milestone 150,000 Structures; Superbugs! How Bacteria Evolve Resistance to Antibiotics; a Molecule of the Month User Survey; and more.
Vote Now for the Viewer's Choice Award
RCSB PDB challenged high school students to create short videos that tell stories about bacterial resistance to aminoglycoside antibiotics.
Award winners will be announced on rcsb.org and pdb101.rcsb.org on May 14, 2019.
Celebrate DNA Day on April 25
DNA Day commemorates the completion of the Human Genome Project in 2003 and the discovery of DNA's double helix in 1953. Celebrate by:
- Creating a paper model of DNA (available in English and Spanish from PDB-101)
- Visiting the National Human Genome Research Institute's DNA Day website for teaching tools, chatroom, and webcasts
- Extracting DNA in your kitchen (strawberries recommended; you can pound them in a plastic bag instead of using the blender)
- Watching the NSF's Chalk Talk: DNA
- Exploring Molecule of the Month features on DNA, Designed DNA Crystal, DNA Polymerase, and more at PDB-101
Spring Newsletter Published
This issue highlights a Milestone 150,000 Structures; Superbugs! How Bacteria Evolve Resistance to Antibiotics; a Molecule of the Month User Survey; and more.
Take the Molecule of the Month User Survey and Enter to Win
RCSB PDB wants to learn more about Molecule of the Month readers worldwide.
High School Students: Submit Antibiotic Resistance Videos Before April 23
Antibiotic resistance is one of today's growing problems. Help increase awareness by participating in the 2019 Video Challenge for High School Students on Mechanisms of Bacterial Resistance to Aminoglycoside Antibiotics.
Molecular Landscapes and the Art of Science
Brain – wider than the sky exhibits artwork about the about the brain for all ages at the Calouste Gulbenkian Museum in Lisbon. Available until June 10th, Brain – wider than the sky features video installations on the brain, interactive sensory exhibits, artworks and digital games to showcase the themes of the exhibition.
New watercolor paintings Excitatory and Inhibitory Synapses by Molecule of the Month creator David Goodsell are on display. Can't make the exhibit? Visit PDB-101 for a new digital gallery of Goodsell's SciArt work.
Goodsell's molecular landscapes are now available from PDB-101 in a special SciArt Digital Archive. These watercolor paintings integrate information from structural biology, microscopy and biophysics to simulate detailed views of the molecular structure of living cells. These illustrations are free for use under CC-BY-4.0 license. Acknowledgement should be given as indicated for each illustration.
The Goodsell Gallery accompanies PDB-101's Irving Geis Digital Archive. Geis (1908-1997) was a gifted artist who helped illuminate the field of structural biology with his iconic images of DNA, hemoglobin, and other important macromolecules. Through a collaboration with the Howard Hughes Medical Institute (HHMI), which owns the Geis Archives, PDB-101 displays many of Geis' illustrations in the context of the corresponding PDB structures and related molecular information. Through this archive, these images are available for download for noncommercial usage.
The PDB Archive Reaches a Significant Milestone
With this week's update, the PDB archive has passed the milestone of 150,000 entries, and now contains a total of 150,145.
Established in 1971, this central, public archive has reached this milestone thanks to the efforts of structural biologists throughout the world who collectively contribute a wealth of experimentally-determined protein and nucleic acid structure data, which is made available to researchers all around the world, across many different disciplines.
Four wwPDB data centers support online access to three-dimensional structures of biological macromolecules that help researchers understand many facets of biomedicine, agriculture, and ecology, from protein synthesis to health and disease to biological energy. The archive is large, containing more than 1.9 million files related to these PDB entries and requiring more than 512 gigabytes of storage.
The archive reached the landmark of 100,000 entries in 2014, the International Year of Crystallography. Since that record was set, the PDB continued to grow rapidly, both in number of deposited structures and in the complexity of the data. This growth has been supported by the launch of OneDep, a common global system for deposition, validation, and biocuration of PDB data for supported experimental methods. The OneDep system and the underlying PDBx/mmCIF archive format enable the PDB archive to adapt over time to meet the challenges posed by developments in structural biology. More than 41,000 structures that have been deposited, annotated, and validated using OneDep have now been released into the PDB archive, with many more entries updated to ensure consistency of the archive.
With this week's regular update, the PDB welcomes 262 new structures into the archive. These structures join others vital to research and education in fundamental biology, biomedicine, and bioenergy. Since its inception, the size of the archive has increased tenfold roughly every 10-15 years: the PDB reached 100 released entries in 1982, 1000 entries in 1993, and 10,000 in the year 2000. Now that the 150,000th is made available, more than half of the archive has been released in the past ten years.
The scientific community eagerly awaits the next 150,000 structures and the invaluable knowledge these new data will bring. However, the increasing number, size and complexity of biological data being deposited in the PDB and the emergence of hybrid structure determination methods constitute major challenges for the management and representation of structural data. wwPDB will continue to work with the community to meet these challenges and ensure that the archive maintains the highest possible standards of quality, integrity, and consistency.
Development and future of the PDB archive and wwPDB organization is described in the new reference publication for the PDB archive: Protein Data Bank: the single global archive for 3D macromolecular structure data (Nucleic Acids Res., 2019) and many other papers, including Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (Methods in Molecular Biology, 2017), How community has shaped the Protein Data Bank (Structure, 2013), and Creating a Community Resource for Protein Science (Protein Science, 2012). A full list is available.
New Video: Penicillin and Antibiotic Resistance
Since its discovery in 1928, penicillin and penicillin-related antibiotics helped save countless lives from bacterial infections. However, in the face of overuse and misuse of antibiotics, bacteria evolved resistance mechanisms that allow them to proliferate even in the presence of the newest antibiotics.
Superbugs! How Bacteria Evolve Resistance to Antibiotics
Antibiotics are one of the miracles of modern medicine, allowing us to fight infection by pathogenic bacteria. Antibiotics attack essential molecular machines in bacteria, stopping or slowing their action and ultimately killing the cell.
Superbugs such as MRSA (Methicillin-resistant Staphylococcus Aureus), have found ways to evade almost all current antibiotics.
Join Our Team as a Biocurator
RCSB PDB is looking for a Biochemical Information & Annotation Specialist to join the RCSB PDB team at Rutgers, The State University of New Jersey.
The Challenge: Curate, validate, and standardize macromolecular structures from the PDB community. Participate in exciting projects with significant impact on the scientific community. This is a unique opportunity to engage in leading edge research, development, and outreach activities of the RCSB PDB with worldwide impact.
New Online Curriculum: The PDB Pipeline & Data Archiving
Drawing from their collective knowledge as structural biologists, data scientists, educators, developers and managers of data resources, the Research Collaboratory for Structural Bioinformatics (RCSB) team has created an open access, modular educational curriculum covering concepts, approaches and requirements for developing and managing the data pipeline for a curated public archive of biological experimental data. The online curriculum, available as part of the RCSB PDB-101 education website and also accessible directly via edsb.rcsb.org, makes best practices recommendations for data resource development and management. The intended audience includes scientists, who can use the materials for self-instruction, as well as librarians and information specialists, who can use the materials to develop training services for students, scientists, and staff. In addition, the curriculum is intended to help accelerate development of new data archives for experimental methods used in Integrative Structural Biology. The curriculum is composed of eight modules that can be studied separately or as a complete online course. Materials include professionally produced videos, powerpoint slides, and exercises that guide students step-by-step to design, create, and query their own data archive. This education development project was funded by National Institutes of Health National Library of Medicine as part of the NIH Big Data to Knowledge (BD2K) Initiative (R25 LM012286).
Education Corner: Improving Visual Literacy
In the Education Corner, Kristen Procko and the BioMolViz Group describe their efforts in Creating Accessible Tools for Molecular Visualization Instruction that are the result of workshops held with broader community of biochemistry, chemistry, and molecular biology educators.
Other newsletter articles in this issue include 2018 milestones and publications, improved support for XFEL/SFX structures, new PDB-101 resources for exploring Molecular Evolution and Antimicrobial Resistance, and more.
Winter Newsletter Published
This issue reviews 2018 milestones and publications, improved support for XFEL/SFX structures, new PDB-101 resources for exploring Molecular Evolution and Antimicrobial Resistance, and more.
2018 FASEB BioArt Winner
PDB-101's video animation of the calcium pump moving ions across a cell membrane was among the 2018 Winners of FASEB's BioArt Competition. This year’s 10 winning images and three videos represent a wide range of biomedical research, from a Human Hand Showing Carpal Tunnel Tendons and Palm Muscles to a Video of Arabidopsis flowers forming at tip of stem.
The Calcium Pump animation is an excerpt from the introductory What is a Protein? video (also the subject of the 2019 calendar). PDB-101 hosts a collection of videos and animations on a variety of topics.
2019: What is a protein?
Proteins play vital roles in all living organisms. Their specific amino acid sequences give proteins their distinct shapes and chemical characteristics. Proteins rely on the recognition of specific 3D molecular shapes to function correctly for DEFENSE, TRANSPORT, ENZYMES, STRUCTURE, STORAGE, and COMMUNICATION.