Atlas of

for MolviZ.Org (Atlas.MolviZ.Org)
Suggestions to Eric Martz.
Last updated: 2016.
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Atlas of Macromolecules by Eric Martz is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
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Lesson Plans

Here is a 2016 syllabus for an 8-hour block (3 afternoons in a computer lab) in a lab course for senior undergraduates. Each student picks a molecule from this Atlas, then reports on how its structure supports its function. The report has eleven sections (questions) and a sample completed report is provided. Feel free to copy/adapt: Proteopedia encourages share-alike re-use with attribution, as does this Atlas (see license at top).

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 usually been selected to avoid complications (such as being very large, lacking sidechains, 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.

Update History/Versions.


Signal Cascade Proteins (Cytoplasmic)

Soluble Proteins (Not Enzymes)


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


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, Nucleosome, Ribosome, etc.)
Virus Capsids
Virus Components (Virus Proteins & Nucleic Acids)

Magnificent Molecular Machines

Immune System & Defense Molecules (Antibody, etc.)

Since these models contain no protein and no nucleic acid chains, the entire model is Ligands+ in FirstGlance. The Vines/Sticks view is useful. Toggle the Ligands+ button to spacefill.  
Unusual Tertiary and Quaternary Structures

Intrinsically Disordered / Natively Unstructured Proteins
Animated Morphs of Conformational Changes


Evolutionary Conservation

History: Earliest Crystallographic Structures

Other Browsable Lists of Molecules

  1. To find the experimental method:
    • In FirstGlance:
      Snapshot from FirstGlance in Jmol showing Method.
      • The method is given in the Molecule Information Tab (the first tab).
    • In Proteopedia:

    Snapshot from FirstGlance in Jmol: View All NMR Models
  2. To see an NMR ensemble of models:
    • FirstGlance shows you, initially, only the first model of the ensemble. If you opt to use Java, there is a link View All Models (in the Molecule Information Tab, which is the first tab).

      20 NMR models.
      Intrinsically Disordered.

      21 NMR models.
      Stable Fold.

  3. Snapshot from FirstGlance in Jmol: links to Biological Unit.
    To see the biological unit: View the structure in FirstGlance. Initially, FirstGlance shows you the asymmetric unit. This is often not the functional form of the molecule, which is called the "biological unit". You can click on the term Biological Unit in FirstGlance for an explanation of these terms. There you will find a link to view the biological unit.

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. For suggestions that have been incorporated, 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. For newer technology, see Note #3.

visits since August 30, 2002. Stats.

Update History: This Atlas contains about 160 macromolecular structures, most published before 2007.

Suggestions to Eric Martz.