News 2022
Molecular Landscapes for 2023
12/31
Season's Greetings
12/22
Celebrate #NationalCrosswordDay with Sequence Events
12/20
Guide to Understanding PDB Data: Hierarchical Structure
12/15
Exploring the Structural Biology of Cancer
12/13
Structural Biology and Nobel Prizes
12/08
Molecular Origami: Green and Red Fluorescent Proteins
12/06
Video: How Neurons Communicate
11/30
Keeping Up with RCSB PDB News
11/22
Molecular Landscapes
11/21
Education Corner: Animating Photosynthesis
11/15
Meet RCSB PDB at ABRCMS
11/07
New Coloring Page: Clathrin-coated Pit
11/04
Molecular Landscapes
11/01
Meet RCSB PDB at SACNAS
10/25
Register Now for Virtual Crash Course: Using KBase to access PDB Structures and CSMs
10/21
Happy Birthday, PDB!
10/19
Happy Birthday, Irving Geis
10/16
Education Corner: Inktober SciArt
10/13
Fall Newsletter Published
10/10
Undergrads/Grads: Apply to the Molecule of the Month Boot Camp (January 2023)
10/07
Structural Biology and Nobel Prizes
10/01
Molecular Origami: Build a 3D paper model of DNA
09/27
Register Now for Virtual Crash Course: Exploring Computed Structure Models from Artificial Intelligence/Machine Learning at RCSB.org
09/07
Explore Computed Structure Models Alongside PDB Data
08/31
Education Corner: Bound! Protein-Drug Card Game
08/29
Molecular Landscapes: E. coli
08/23
Poster Prize Awarded at ACA
08/09
Congratulations to David S. Goodsell
08/01
New Coloring Page
07/31
Poster Prize Awarded at ISMB
07/19
Summer Newsletter Published
07/12
New Position: Senior Front-end Web Developer
07/12
Congratulations to David S. Goodsell
07/08
Education Corner: Python Scripting for Biochemistry & Molecular Biology
06/21
Learn to Use Mol* for 3D Visualization
06/14
New Flyer: Poxviruses
06/06
Play the Bound! Protein-Drug Card Game
06/01
Watch PDB50 Celebrations
05/24
Award-Winning Videos on Molecular Mechanisms of Cancer
05/17
Postdocs and Scientific Software Developers
05/16
Curated Files for 3D Printing
05/10
Vote Now for the Viewer's Choice Award
05/03
Videos of Experimental Methods
04/22
Spring Newsletter Published
04/19
High School Students: Submit Videos By April 25
04/15
Paper Published: Evolution of the SARS-CoV-2 proteome in 3D
04/12
New Coloring Pages
03/31
Meet RCSB PDB at ASBMB
03/28
Annual Report Published
03/24
Video: Opioids and Pain Signaling
03/17
Brain Awareness Week
03/15
Award-Winning Images
03/14
Register for Exploring Structural Database Use in Crystallography
03/08
Molecular Landscapes in The New Yorker
03/01
Molecule of the Month Newsletter
02/22
Molecular Landscapes
02/15
Molecular Valentines
02/11
Education Corner: Inktober SciArt
02/08
Register Now for Crash Course: Python Scripting for Biochemistry & Molecular Biology
02/01
New Publications in Protein Science
01/25
New Publication in Structure
01/18
Winter Newsletter Published
01/12
2022: Revolutionizing Structural Biology with 3DEM
01/01

Guide to Understanding PDB Data: Hierarchical Structure

12/15 

<I>Atomic representations are shown at left, and cartoon representations are shown at left. Alpha helices form spring-shaped structures with each amino acid forming a hydrogen bond with an amino acid further down the chain. Beta strands are extended regions of the chain that form hydrogen bonds with neighboring beta strands, forming a beta sheet. In this structure, four beta strands form the sheet with neighboring strands running in opposite directions, as shown by the cartoon arrows. Note that in these illustrations, side chains are not shown on each amino acid, to make it easier to see the backbone structure. Structures taken from PDB ID 1ic2 and 4gcr.</I>Atomic representations are shown at left, and cartoon representations are shown at left. Alpha helices form spring-shaped structures with each amino acid forming a hydrogen bond with an amino acid further down the chain. Beta strands are extended regions of the chain that form hydrogen bonds with neighboring beta strands, forming a beta sheet. In this structure, four beta strands form the sheet with neighboring strands running in opposite directions, as shown by the cartoon arrows. Note that in these illustrations, side chains are not shown on each amino acid, to make it easier to see the backbone structure. Structures taken from PDB ID 1ic2 and 4gcr.

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.

PDB-101's Guide to Understanding PDB Data 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 new chapter highlights the Hierarchical Structure of Proteins. Topics in this article include:

  • Why is Understanding Protein Folding Important?
  • Hierarchical Structure
  • Visualization of Hierarchical Structure
  • Classifying Protein Folds

Visit PDB-101 for more.


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