Atlas of
Macromolecules

for Protein Explorer
Suggestions to Eric Martz.
All images copyright © 2002 by Eric Martz.
Click on any image for more information.


Contents
Lesson Plans

Four ways to use the PDB ID codes below:

  1. Simply click on the hyperlink below -- it will start Protein Explorer and display the molecule you have selected automatically (provided you are connected to the Internet);
  2. At the FrontDoor of Protein Explorer (www.proteinexplorer.org), enter the PDB identification code into the slot;
  3. Distribute to your students the PDB identification codes you have selected from the Atlas or elsewhere. (See also Lesson Plans to your right.)
  4. Make a web page of hyperlinks to molecules you have selected in the Atlas. Open free Netscape Composer (or any other HTML editor), choose a molecule in the Atlas, and drag its hyperlink from the Atlas into the Composer. Here are detailed instructions.

To find the primary literature citation for a molecule, the full name and species from which it came, etc., after displaying the molecule in PE, go to PE's Features of the Molecule.

Years in parentheses after links to molecules indicate the years of publication. In some cases a range of years is given: the early year is when the molecule was first solved (if I happen to know that) at 3.5 Å resolution or better; the later year is when the structure chosen for the Atlas was published.

In each category below, PDB files have been divided into those that are relatively straightforward, those that are more challenging, and sometimes enormous. "Straightforward" cases have been selected to avoid complications (such as being NMR ensembles, lacking sidechains, having a nonstandard file format, having many alternative sidechain conformations, etc.).

  Lesson Plans: It is best if your students first have one to two hours to do the 1-Hour Tour to become familiar with Protein Explorer (PE). Then you can assign molecules from the list below to each group of students (or let them pick), and hand out Discovery in Protein Explorer, a generic set of questions, some open-ended. Optionally, you can provide hints suggesting how to use PE to answer the questions. If you use PE in your class, please do the Student Assessment of Learning Gains.

Acknowledgements. Some cases in the Atlas came from Tim Herman and Michael Patrick's 2001 SEPA Course. Thanks to PDB Files for Teaching Biochemistry by Don Harden and Dabney Dixon of Georgia State University, and Molecule of the Month by David Goodsell for some of the cases below. For suggestions that have been incorporated below, thanks also to Ilan Samish, David Margulies, and Bruce Southey. Thanks to the EBI Probable Quaternary Structures server by Kim Henrick and Janet Thornton which has been invaluable in many cases below.

 
Enzymes

 
Signal Cascade Proteins (Cytoplasmic)

 
Soluble Proteins (Not Enzymes)

 
Toxins

 
Structural Proteins

 
Calcium-Binding Proteins

 
Lipid Bilayers
(Yes, we know they're not really macromolecules.)
 
Integral Membrane Proteins

 
Myristoylated Proteins
Recoverin 1iku...1jsa

 
DNA and RNA

Genes were shown to reside in DNA in 1944 (Avery et al.) and this became widely accepted after the 1952 experiments of Hershey and Chase. The double helical structure of the DNA was predicted by James Watson and Francis Crick in 1953 (Nobel Prize, 1962). Their prediction was based in part upon X-ray diffraction studies by Rosalind Franklin, to whom Watson and Maurice Wilkins gave inadequate credit (see Rosalind Franklin: Dark Lady of DNA by Brenda Maddox, HarperCollins, 2002). The predicted B-form double helix was not confirmed with atomic-resolution crystal structures until 1973, first by using dinucleotides of RNA (Rosenberg et al.). The first crystal structure containing more than a full turn of the double helix was not solved until 1980 (Wing et al. 1BNA, 1981, 12 base pairs). The lag of more than a quarter century between prediction and empirical confirmation involved development of X-ray crystallography for macromolecules, and the need to produce a short, defined sequence of DNA for crystallization. This brief account is based upon a review by Berman, Gelbin, and Westbrook (Prog. Biophys. molec. Biol. 66:255, 1996), where the references will be found.


 
Proteins Complexed to Nucleic Acids (Transcription Factors, Polymerases, etc.)
 
Virus Capsids

 
Magnificent Molecular Machines

 
Immune System & Defense Molecules (Antibody, etc.)
 
Carbohydrates
 
Unusual Tertiary and Quaternary Structures

 
Animated Morphs of Conformational Changes

 
Evolutionary Conservation

 
Protein Crystals

 
History: Earliest Crystallographic Structures

 
Other Browsable Lists of Molecules


Suggestions to Eric Martz.
 
* PDB file sizes marked "*" are given for gzipped files, as they will be transferred from the Protein Data Bank (or other servers) to Chime when the above links are clicked. If you save the plain text PDB file to disk from Chime/PE, it will be about 4-fold larger.
 
Alpha-carbons only: Some very large structures are supplied as alpha-carbons only. This enables the backbone to be viewed, but not secondary structure (and therefore also not schematic "cartoon" rendering). To see secondary structure, you'll have to get the complete structure (usually available from EBI's Probable Quaternary Structures), but it is typically multiple megabytes in size.