Muscular dystrophy, cancer, botulism, sleeping sickness, schizophrenia, bird flu, spinal muscular atrophy, HIV/AIDS, multiple sclerosis. Scientists throughout the world jump-start their research into how the body fights off or falls prey to disease by accessing molecular data from the Protein Data Bank (PDB).
The Molecule of the Month column presents a different molecule from the PDB each month, introducing the molecule's function and describing its importance to health and technology.
Created by scientist-artist David Goodsell, each column includes three-dimensional graphics that let visitors view the molecule from all angles. Over 150 installments are now available online, covering topics from viruses to genetics to nanotechnology. Learn more.
The National Institutes of Health awarded $47.5 million to Rutgers to advance groundbreaking research on protein structures.
Of this amount, $12.5 million went to the Structural Biology Knowledgebase, also led by professor Helen M. Berman, which integrates the results of structural biology and genomics efforts with other publicly available biological information (including the PDB) to facilitate further research.
A consortium led by Rutgers professor Gaetano Montelione received $35 million to advance the complex techniques used to determine such structures. Learn more.
RU-tv’s student producer Alex Proulx visits the RCSB PDB on Rutgers' Busch Campus to ask its director, Helen Berman, what it’s all about.
This repository, administered by Rutgers, holds much of the world’s knowledge on the large molecules that are the building blocks of life itself. Understanding the shape of these structures aids in understanding how they function in the body, ultimately leading to scientific breakthrough and drug discovery.
The PDB gathers biological data from scientists around the world who have determined the three-dimensional atomic structures of large molecules through painstaking and time-consuming research. Rutgers scientists confirm, standardize, and annotate the complex biological information.
They then turn around and make all this knowledge universally available via the internet. It’s a digital laboratory built on global cooperation and knowledge sharing, coordinated at Rutgers.
“We’re here to provide reliable storage and access to molecular data, which in turn drives scientific discovery and education in a variety of fields, ” says Helen M. Berman, Board of Governors professor of chemistry and chemical biology, and director of the Research Collaboratory for Structural Bioinformatics (RCSB), which oversees the PDB. The RCSB PDB is a collaboration between Rutgers and the University of California, San Diego. “We also develop tools and resources that help students of all ages explore biology at the molecular level.”
Most people are familiar with the classic double-helix structure of DNA, which was discovered in 1953. Find out more about DNA.
These are just a few examples of the over 70,000 molecular structures archived in the PDB. They have been determined by scientists around the world through experiments using X-ray crystallography, nuclear magnetic resonance, and electron microscopy.
Online visitors to the PDB website can navigate through the Molecule of the Month columns according to these six biological categories (and then by subcategories), as well as by date and column title. This makes it possible for users to search the columns based on their biological interest, without having a specific molecule in mind.
The enlarged area in this image of hemoglobin shows the molecule binding to oxygen. Find out more about hemoglobin.
Many PDB structures illustrate different drug-protein interactions in the body. For more information, you can download the How Do Drugs Work? poster.
The PDB contains information about large and complex structures, such as the highly destructive ubiquitin proteasome. Proteasomes are voracious protein shredders that dismantle obsolete proteins that have been tagged for destruction.
This image, from the Molecule of the Month column on collagen, illustrates the rope-like fibrils made up of several different types of collagen molecules that crisscross to form a tough surface to support the skin and many internal organs.
Vault proteins form a symmetrical shell with a hollow compartment inside. This one is from a rat liver cell. Vaults are found in many different types of cells, but exactly what they do remains a mystery to researchers.
Protein structures are extraordinarily diverse. The daisy in the center above is glutamine synthetase, an essential enzyme that controls the use of nitrogen in cells, while the piece of knitted fabric third from the right is a microtubule, which among many other functions provides scaffolding for cell walls.
The RCSB PDB sponsors a traveling art exhibit, shown here on display at Rutgers Alumni Weekend. In the past, the exhibit has traveled to Germany and India, as well as to locations in the United States.
The PDB got its start at Brookhaven National Laboratory in 1971 with a handful of protein structures. A $10 million grant from the National Science Foundation, the National Institutes of Health, and the U.S. Department of Energy underwrote the data bank’s move to Rutgers in 1998. The archive, considered “vast” at the time, contained about 8,000 structures.
Subsequent five-year grants of $30 million each were awarded in 2004 and again in 2009 to continue the PDB’s expansion. Little more than 12 years after its relocation to Rutgers, the PDB now contains more than 77,000 proteins, nucleic acids, and complex assemblies.
Since 2003, the PDB archive has been supported by a unique scientific collaboration called the Worldwide Protein Data Bank (wwPDB). Its purpose is to ensure that the PDB archive, now and in the future, is freely and publicly available to the global community. The four wwPDB members in the United States, Europe, and Asia host deposition, processing, and distribution centers for PDB data and collaborate on a variety of projects and outreach efforts.
Last year, the wwPDB received more than 8,900 new structures, supplied by an international cadre of researchers—nearly half coming from the United States, more than a quarter from Europe, 16 percent from Asia, 7 percent from Australia/New Zealand, 1 percent each from Africa and South America, and 7 percent from industry sources. During the same time period, more than 300 million data files from the member sites were downloaded or viewed online.
Today, scientists from around the world depend upon PDB data for their research and discoveries, while students and teachers use the wealth of educational material on the PDB’s website to learn about the wonders of biological function at the molecular level.
