Atlas of
Macromolecules

for MolviZ.Org (Atlas.MolviZ.Org)
Suggestions to Eric Martz.
All images copyright © 2002-2006 by Eric Martz.
Click on any image for more information.






Contents
Lesson Plans




Teachers: Proteopedia offers an article on Teaching Strategies that includes suggested lesson plans.

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.).

Below, 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.

History: This Atlas contains about 160 macromolecular structures, all published before 2007. It was created in February, 2002, as part of the (now defunct) Protein Explorer project. In 2008, it was restructured to offer links to Proteopedia and FirstGlance in Jmol. In September, 2012, it was restructured to eliminate links and references to Protein Explorer.

 
Enzymes

 
Signal Cascade Proteins (Cytoplasmic)

 
Soluble Proteins (Not Enzymes)

 
Toxins

 
Structural & Motility Proteins

 
Calcium-Binding Proteins

 
Lipid Bilayers & Water
(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. 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
 
Virus Components (Virus Proteins & Nucleic Acids)

 
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.


Notes:
  1. To find the experimental method:
  2. To see an NMR ensemble of models:
  3. Most of the biological units in this Atlas (filenames ending in .mmol) were obtained from the Probable Quaternary Structure server of the European Bioinformatics Institute. However, this server stopped adding new structures in August, 2009.

    Currently (2012), the Biological Unit (functional quaternary structure) can be obtained most easily from the MakeMultimer Server.


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 was invaluable in many cases below. For newer technology, see Note #3.