News 2018
Summer Newsletter Published
07/10/2018
PDB Trends: Expanding Boundaries of Complexity with 3DEM
07/03/2018
Facing Rising Temperatures?
07/02/2018
Award-Winning Videos on Antibiotic Resistance
06/12/2018
Vote Now for the Viewer's Choice Award
05/31/2018
Molecular Origami: Build a 3D model of Human Papillomavirus (HPV)
05/27/2018
Guide to Understanding PDB Data
05/22/2018
Creating Protein Sculptures
05/15/2018
Video Answers "What is a Protein?"
05/08/2018
Advisor Wins 2018 Tyler Prize for Environmental Achievement
05/01/2018
Meet RCSB PDB at Rutgers Day (April 28)
04/26/2018
Celebrate DNA Day on April 25
04/23/2018
Meet RCSB PDB at ASBMB
04/20/2018
Helen Berman Elected to American Academy of Arts and Sciences
04/19/2018
2017 Video Challenge Deadline: May 23
04/15/2018
Spring Newsletter Published
04/10/2018
Access Irving Geis' Early Molecular Images in 3D
04/10/2018
Video: How Enzymes Work
03/20/2018
Enter to Win the AMR Calendar
03/13/2018
Enter the 2017 Video Challenge
03/06/2018
Meet RCSB PDB at AAAS
02/13/2018
Special Issue Focused on Tools for Protein Science
01/30/2018
From the PDB to Phoenix: My Journey as an RCSB PDB Intern
01/23/2018
Winter Newsletter Published
01/16/2018
A Year of Antimicrobial Resistance
01/02/2018

Summer Newsletter Published

07/10/2018

The Summer 2018 issue of the RCSB PDB Newsletter is now online.

This issue looks at summer meetings and events, OneDep improvements for data replacement, download and display of electron density maps, and more. Award-winning videos on antibiotic resistance from the RCSB PDB High School Challenge are highlighted.

The Education Corner by Leah Cairns (Johns Hopkins University School of Medicine) follows a journey From Structural Biology to Science Policy.

RCSB PDB Newsletters and Education Corners are published and archived online.


PDB Trends: Expanding Boundaries of Complexity with 3DEM

07/03/2018

3D electron microscopy (3DEM) is revolutionizing the field of structural biology. Atomic structures of biomolecules are now being determined by 3DEM, due to recent advances in several key technologies, including methods for sample preservation, vastly improved microscopy optics and detectors, and novel methods for structure solution with advanced computing. Researchers are also taking an integrative approach, determining atomic structures of subunits with X-ray crystallography and NMR spectroscopy, then using them to build a large assembly based on data from 3DEM. 3DEM is proving to be a perfect complement to X-ray and NMR techniques, since 3DEM is most effective on large, complex assemblies, which are typically difficult to study by other methods, and does not require large quantities of material, homogeneous samples, or crystallization.

Structures from 3DEM are made publicly available in the PDB archive to help further scientific research and education. The PDB released its first 3DEM entry in 1991, the ground-breaking structure of bacteriorhodopsin. Since then, more than 2,100 3DEM structures have been made available in the PDB archive, with more than 1000 released from 2015-2017.


Facing Rising Temperatures?

07/02/2018

RCSB PDB News ImageSmall toxic peptides help protect us from bacterial infection

Bacteria are a constant threat, so our bodies have many defenses to protect us from infection. One of our first lines of defense is a collection of small peptides, termed antimicrobial peptides, that are secreted from our cells. These peptides are toxic to a broad spectrum of bacteria, binding to their membranes and disrupting their function. For instance, dermcidin is an antimicrobial peptide secreted by sweat glands that attacks any bacteria on our skin. The active form of the peptide is 47 amino acids long. As seen in the crystal structure (PDB structure 2ymk), it folds into a long alpha helix, and then six copies of the peptide assemble to form a pore that penetrates the bacterial membrane. This allows ions to flood across the cell membrane, ultimately killing the cell.

More at Molecule of the Month on Dermcidin.


Award-Winning Videos on Antibiotic Resistance

06/12/2018

The fifth edition of the Video Challenge for High School Students again demonstrates creativity in storytelling and science communication. This year's challenge focused on the mechanisms of bacterial resistance to beta-lactam antibiotics. All submitted entries can be viewed online.

Our panel of expert judges has 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.

Congratulations to the 2018 Winning Videos:

  • First Place: Beta-Lactam Resistance: The Pandemic of Tomorrow by Chelsea Okocha, Serena Wang, and Angela Song of West Windsor-Plainsboro High School South in Princeton Junction, NJ (Team Advisor: Karel Marshall)
  • Second Place: Toby the Superbug: Origin Story By Chris Boodram, Michelle Li, and Leia Park of Stuyvesant High School, New York, NY (Team Advisor: Gilbert Papagayo)
  • Third Place: Resistance to Beta-lactam Antibiotics in Bacteria By Vanessa Lu, William Dang, Ethan Du, and Jason Le of Mira Mesa High School, San Diego, CA (Team Advisor: Lisa Yoneda)
  • Viewer's Choice: The Beta-lactam Antibiotic Crisis By Sohil Dharia and Michael Dicpinigaitis of Jericho High School, Jericho, NY (Team Advisor: Michael Giallorenzo)

Many thanks to the expert judges, students, teachers, parents, judges, and voters who made this exciting competition happen!


Vote Now for the Viewer's Choice Award

05/31/2018

RCSB PDB recently challenged high school students to create short videos telling stories about the bacterial resistance to the beta-lactam antibiotics. Watch the challenge entries online and cast your vote now for your favorite video.

Voting for the Viewers Choice Award is now open until June 6th 12:59 EST. Winners will be announced at PDB-101 and rcsb.org on June 12, 2018.


Molecular Origami: Build a 3D model of Human Papillomavirus (HPV)

05/27/2018

Papillomaviruses are annoying pests that occasionally turn into deadly dangers. They attack cells in our skin and mucous membranes. When they infect cells, they ramp up the normal growth functions, often forming warts. Usually our defenses are able to get the infection under control, but in some exceptional cases, the virus persists and the unwanted growth can turn into cancer. Alarmingly, infection by a few particularly-virulent types of papillomavirus is the leading cause of cervical cancer. Fortunately, by studying these viruses, scientists have discovered highly effective ways to fight them.

Papillomavirus is a small virus, with a simple capsid surrounding a circular DNA genome. The includes 360 copies of the major capsid chain, called L1. A second capsid chain, called L2, is found on the inside and may help with packaging the genome. The capsid structure, however, is not a typical quasisymmetrical virus. Instead, like simian virus 40, the L1 chains form 72 pentameric “capsomeres”, which then interact with one another through long flexible tails.

To build paper model of Papillomavirus, download and print the template PDF. Instructions for cutting and assembling are included.

Use the PDB-101 Browser to explore more resources and articles about viruses.


Guide to Understanding PDB Data

05/22/2018

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.

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.

Topics include

RCSB PDB News ImageFrom Methods for Determining Atomic Structures: Structures of photoactive yellow protein were determined by serial femtosecond crystallography after illumination, capturing the isomerization of the chromophore after it absorbs light. Structures included in this movie include: 5hd3 (ground state), 5hdc (100-400 femtoseconds after illumination), 5hdd (800-1200 femtoseconds), 5hds (3 picoseconds), 4b9o (100 picoseconds), 5hd5 (200 nanoseconds) and 1ts0 (1 millisecond). For more, see Molecule of the Month on Photoactive Yellow Protein.


Creating Protein Sculptures

05/15/2018

In the latest Newsletter, Keagan O’Mara (@MisterOMara, Bio-Med Science Academy STEM School) describes making protein models with his Environmental Engineering class.

RCSB PDB News Image

Read more on Creating sculptural models of proteins in a high-school engineering in the Education Corner

Other articles look at the impact of the PDB archive as described in a new Protein Science publication, highlights new and updated Validation Reports, and announces new features available at RCSB.org. Information about the High School Video Challenge focused on antimicrobial resistance is also available. More at the Spring 2018 Newsletter.


Video Answers "What is a Protein?"

05/08/2018

In 2013, PDB-101 released its first molecular animation, What is a Protein?. Since then, that video has been viewed more than 450,000 times.

PDB-101 has continued to publish many more videos and animations, including How Enzymes Work and A Molecular View of HIV Therapy.

Building upon the success of these new features, What is a Protein? was recently been updated and improved. Watch it now at PDB-101.

RCSB PDB News Image
RCSB PDB News Image
RCSB PDB News Image

A related PDF Flyer is also available for download from PDB-101.


Advisor Wins 2018 Tyler Prize for Environmental Achievement

05/01/2018

Rutgers Distinguished Professor Paul Falkowski, RCSB PDB Advisory Committee Member, will be presented the Tyler Prize for Environment Achievement in a ceremony in Washington D.C. on May 3, 2018.

The 2018 Tyler Prize for Environmental Achievement – often described as the ‘Nobel Prize for the Environment’ – has been awarded to Paul Falkowski and James J. McCarthy, for their decades of leadership in understanding – and communicating – the impacts of climate change. Paul Falkowski, one of the world’s greatest pioneers in the field of biological oceanography, is a Rutgers distinguished professor in the departments of Earth and Planetary Sciences and Marine and Coastal Sciences and is the founding director of the Rutgers Energy Institute. James J. McCarthy is from the Department of Biological Oceanography at Harvard University.

RCSB PDB News ImageSome proteins have played key roles in the environment: some were involved in global changes millions of years ago, and some are affecting the environment today. By understanding these molecules, we can manage our impact on the environment more effectively. More at PDB-101.


Meet RCSB PDB at Rutgers Day (April 28)

04/26/2018

Rutgers Day is a full day of discovery and lively activities that showcase the varied resources, departments, and people at the university. Learn about the Protein Data Bank, Health, and You with at the RCSB PDB Molecular Candy Lab in the Life Sciences area on Busch Campus (BLSA-224). Explore biology at the molecular level by building virus and DNA models with your favorite candy.

RCSB PDB News Image


Celebrate DNA Day on April 25

04/23/2018

National DNA Day is celebrating the 15th anniversary of the completion of the Human Genome Project in 2018! On April 25th, students, teachers and the public can learn more about how advances in genetics and genomics have changed people's lives and what the future holds.

Celebrate by:

RCSB PDB News ImageEach cell includes a DNA genome that encodes the instructions for building all of the cell's proteins. Atomic structures have revealed many of the molecular machines that protect and replicate this DNA, transcribe it into RNA, and translate it into proteins. Learn more at PDB-101


Meet RCSB PDB at ASBMB

04/20/2018

Meet RCSB PDB at the American Society for Biochemistry and Molecular Biology (ASBMB) meeting that will take place during Experimental Biology 2018 (April 21-25 in San Diego).

RCSB PDB News ImageLearn about PDB-101 and other activities during Saturday's Science Outreach Activity Poster Session to be held during the Welcome Reception.
RCSB PDB News ImageIntern Priscilla Marie Salcedo will describe how she is Correlating Enzymes in Antimicrobial Resistance in the PDB during the Saturday undergraduate and Tuesday poster sessions.
RCSB PDB News ImageLearn how RCSB PDB is Sustaining A Living Digital Data Resource That Enables Breakthroughs in Scientific Research and Biomedical Education at Monday's poster session


Helen Berman Elected to American Academy of Arts and Sciences

04/19/2018

RCSB PDB News ImageRCSB PDB Director Emerita Helen M. Berman

Helen M. Berman, RCSB PDB Director Emerita and Board of Governors distinguished professor emerita of chemistry and chemical Biology at Rutgers University–New Brunswick, has been elected to the American Academy of Arts and Sciences.

Berman is among 213 people elected to the academy this year, including author Ta-Nehisi Coates, actor Tom Hanks, President Barack Obama, Supreme Court Justice Sonia Sotomayor, gene editing developer Feng Zhang and pediatric neurologist Huda Zoghbi.

Founded in 1780, the academy honors scholars, leaders, artists and innovators and engages them in sharing knowledge and addressing challenges facing the world. The academy’s projects and publications generate ideas and offer recommendations to advance the public good in the arts, citizenship, education, energy, government, the humanities, international relations, science and more.

In 1971, Berman cofounded the Protein Data Bank (PDB) – the international archive of the structures of biological macromolecules. She directed the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), a member of the Worldwide Protein Data Bank, from 1998 to 2014. Berman, who worked in the School of Arts and Sciences, plays a leadership role for the Electron Microscopy Data Resource (EMDR) and is currently developing infrastructure for archiving structures that have been determined using integrative/hybrid methods. Her work on structural bioinformatics has been informed by her research in structural biology, where she focused on nucleic acids, protein nucleic acid complexes, collagen and hydration of macromolecules. Currently, she is making documentary films that communicate the importance of structural biology in medicine and health.

During her nearly 50-year career, Berman has won numerous honors. She is a fellow of the International Society for Computational Biology, the American Association for the Advancement of Science, the Biophysical Society and the American Crystallographic Association. She received the Distinguished Service Award from the Biophysical Society in 2000; the Carl Brändén Award from the Protein Society in 2012; the DeLano Award for Computational Biosciences from the American Society for Biochemistry and Molecular Biology in 2013; and the Benjamin Franklin Award for Open Access in the Life Sciences in 2014.

The newly elected academy members include 36 international honorary members from 20 countries. They will be inducted at a ceremony in October in Cambridge, Massachusetts. Their signatures will be recorded in the Book of Members, joining Benjamin Franklin (1781), Alexander Hamilton (1791), Ralph Waldo Emerson (1864), Maria Mitchell (1848), Charles Darwin (1874), Albert Einstein (1924), Robert Frost (1931), Margaret Mead (1948), Milton Friedman (1959) and Martin Luther King Jr. (1966).


2017 Video Challenge Deadline: May 23

04/15/2018

RCSB PDB News Image

Antibiotics have saved millions of lives, but misuse and overuse has caused an emergence of new and resistant bacteria that threaten our ability to treat common infectious diseases. RCSB PDB invites high school students across the USA to study the molecular mechanisms behind the resistance, create a short video, and submit to our annual challenge. To learn more, visit PDB-101.

The deadline for submissions is May 23. Award winners will be announced on June 12, 2018.


Spring Newsletter Published

04/10/2018

The Spring 2018 issue of the RCSB PDB Newsletter is now online.

This issue looks at the impact of the PDB archive as described in a new Protein Science publication, highlights new and updated Validation Reports, and announces new features available at RCSB.org. Information about the High School Video Challenge focused on antimicrobial resistance is also available.

The Education Corner features Creating sculptural models of proteins in a high-school engineering class by Keagan O’Mara, Bio-Med Science Academy STEM School.

The RCSB PDB Newsletter is published and archived online.


Access Irving Geis' Early Molecular Images in 3D

04/10/2018

RCSB PDB News ImageMyoglobin Fold (1987). Used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved.
RCSB PDB News ImagePhoto by Sandy Geis

Irving Geis (October 18, 1908-July 22, 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, RCSB PDB has established a digital archive of Geis' molecular art. This resource displays many of Geis' illustrations in the context of the corresponding PDB structures and related molecular information. These images are also made available for download for noncommercial usage.

Under the direction of RCSB PDB team members, the Geis Digital Archive is being developed by undergraduates. Students created modern visualizations of the molecules featured in Geis' work, and researched the structures to provide background and supporting information about the illustrations. Alex Alvarado (University of Southern California) and Nicole Werpachowski (Fordham College at Lincoln Center) created the initial design of the resource as part of their Rutgers RiSE (Research in Science and Engineering) experience. Their work was funded during the summer of 2015 by an NSF REU. Rutgers students Belle Lin (2015-2016) and Christopher Markosian (2015-2016) continued work on the project. In 2016, Raheel Ahmad (Rutgers), Pamela Amechi (University of Maryland Baltimore Country), and Keyerra Daniels (Winthrop University) expanded the archive as part of the Rutgers RiSE program.

Thanks to the Howard Hughes Medical Institute for their work on this project. Questions about the HHMI Geis Archives should be sent to archives@hhmi.org.

RCSB PDB News ImageImage of Lysozyme by Irving Geis. Used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved.
RCSB PDB News ImageImage of PDB ID 1LYZ can be launched in 3D using Jmol.
RCSB PDB News ImageAlex Alvarado, Sandy Geis (Irving's daughter), and Nicole Werpachowski
RCSB PDB News ImageBelle Lin and Christopher Markosian
RCSB PDB News ImageKeyerra Daniels, Raheel Ahmad, and Pamela Amechi


Video: How Enzymes Work

03/20/2018

RCSB PDB News Image

Every second inside every living cell, thousands of chemical reactions are taking place. These reactions constitute the essential tasks of life such as metabolism, protein synthesis, cell renewal and growth.

Learn how the proteins called enzymes work to maintain the rate of these reactions at a life-sustaining level in this video hosted by PDB-101.

Explore the PDB-101 Browser to learn more about enzymes.


Enter to Win the AMR Calendar

03/13/2018

RCSB PDB News Image

Antibiotics have saved countless lives, but pathogens are quickly finding ways to survive antibiotic treatment. Antibiotic-resistant bacteria are predicted to become the leading cause of death worldwide, with an expected death rate of 10 million people annually by 2050. They take many approaches: pumping antibiotics out of their cells, altering the molecular machinery that the antibiotics target, and attacking the antibiotics directly. Atomic structures publicly available in the PDB are revealing the details of drug resistance and providing new ways to combat it.

RCSB PDB News ImageEnter to win a printed copy by sending your address via the Contact Us button.

This calendar was created by the RCSB PDB and Jenna Abyad (Drew University) and Priscilla Salcedo (California State University, Northridge) as part of a summer internship with RCSB PDB as described in our Newsletter.

Enter to win a printed copy by sending your address via the Contact Us button, or download in PDF or PowerPoint formats.


Enter the 2017 Video Challenge

03/06/2018

RCSB PDB News Image

Antibiotics have saved millions of lives, but misuse and overuse has caused an emergence of new and resistant bacteria that threaten our ability to treat common infectious diseases. RCSB PDB invites high school students across the USA to study the molecular mechanisms behind the resistance, create a short video, and submit to our annual challenge. To learn more, visit PDB-101.

The deadline for submissions is May 23. Award winners will be announced on June 12, 2018.


Meet RCSB PDB at AAAS

02/13/2018

Meet RCSB PDB at the AAAS Annual Meeting February 15-19 in Austin, TX.

Learn how RCSB PDB is Sustaining A Living Digital Data Resource That Enables Breakthroughs in Scientific Research and Biomedical Education at Sunday's poster session at 2:55pm.

RCSB PDB News Image


Special Issue Focused on Tools for Protein Science

01/30/2018

Protein Science has devoted a special issue (and introduced a new journal article category) to the many modern tools and resources available to researchers interested in the study of proteins and other macromolecules.

Tools for Protein Science highlights computational resources for structure determination, visualization and analysis, molecular modeling, sequence analysis, and analyzing cellular proteins.

In this issue, the article RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education explores the impact of open and accessible PDB data on research, clinical medicine, education, and the economy.

As detailed in the article, the PDB Archive

  • Grows at rate of 10% per year
  • Is used to download 1.8 million structure data files per day
  • Managed by international collaboration (wwPDB)
  • Serves as a model for how “Big Data” can be effectively managed as a public good

PDB Data

  • Enable research in journal subject areas from Agriculture to Zoology
  • Are directly cited in the scientific literature more than 2.6 million times
  • Used by >400 biological data resources

US-funded PDB structures were cited >1 million times in the scientific literature

NSF-funded structures that highlight Fundamental Biology and more have been cited ~56K times

RCSB PDB News ImageHuman dopamine D3 receptor (PDB 3pbl) has been cited by 620 publications and downloaded 178K times

NIH-funded structures that increase understanding of Biomedicine and more have been cited ~874K times

RCSB PDB News ImageBovine Rhodopsin (PDB 1f88) has been cited by 4,122 publications and downloaded 256K times. It is the #3 top-cited PDB structure

DoE-funded structures illuminating Energy and more have been cited ~104K times,

RCSB PDB News ImagePhotosystem I (PDB 3pcq) has been cited by 754 publications and downloaded 38K times

As of May 2017


From the PDB to Phoenix: My Journey as an RCSB PDB Intern

01/23/2018

In the latest Newsletter, RCSB PDB interns describe their journey from summer research to presenting their work at ABRCMS.

Jenna and Priscilla spent the summer of 2017 at the RCSB PDB with support from an NSF Research Experience for Undergraduates (REU). Their work focused on exploring PDB structures related to antimicrobial resistance. Identification of these structures helps researchers understand antibiotic inactivation and drug resistance. Their insights from the summer included suggestions for how to improve the presentation of antibiotic resistance-related PDB structures on RCSB.org, and also led to the development of the 2018 RCSB PDB Calendar. Their work provided them with another opportunity: poster presentations at the 2017 Annual Biomedical Research Conference for Minority Students (ABRCMS).

Their research was part of the RISE (Research Intensive Summer Experience) at Rutgers program. RISE is a nationally acclaimed summer research program for outstanding undergraduates from diverse backgrounds. Scholars participate in 10 weeks of cutting-edge research in the biological, physical, and social/ behavioral sciences, math, engineering, and exciting interdisciplinary areas under the guidance of carefully matched faculty mentors. A comprehensive professional development component, including GRE preparation, complements the research. Apply for RISE and you may wind up working with the RCSB PDB!

RCSB PDB News ImageJenna Abyad is currently a senior at Drew University majoring in Biochemistry and Molecular Biology
RCSB PDB News ImagePriscilla Marie Salcedo is a junior at California State University Northridge majoring in Microbiology.


Winter Newsletter Published

01/16/2018

The Winter 2018 issue of the RCSB PDB Newsletter is now online.

This issue reviews 2017 milestones and publications, improved text searching, and implementation of versioning for PDB data files.

In the Education Corner, RCSB PDB summer interns describe their journey to presenting their work at the ABRCMS meeting.

The RCSB PDB Newsletter is published and archived online.


A Year of Antimicrobial Resistance

01/02/2018

RCSB PDB News Image

Antibiotics have saved countless lives, but pathogens are quickly finding ways to survive antibiotic treatment. Antibiotic-resistant bacteria are predicted to become the leading cause of death worldwide, with an expected death rate of 10 million people annually by 2050. They take many approaches: pumping antibiotics out of their cells, altering the molecular machinery that the antibiotics target, and attacking the antibiotics directly. Atomic structures publicly available in the PDB are revealing the details of drug resistance and providing new ways to combat it.

RCSB PDB News ImageDownload PDF | PowerPoint

This calendar was created by the RCSB PDB and Jenna Abyad (Drew University) and Priscilla Salcedo (California State University, Northridge) as part of a summer internship with RCSB PDB.

PDB-101 offers many other materials focused on Antimicrobial Resistance.


Past news and events have been reported at the RCSB PDB website and past Newsletters.