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Select Molecule options

These options may allow selection of the entire molecule, subcomponent molecules (for example protein vs nucleic acid), or smaller molecular components (cofactors, carbohydrates, specific nitrogenous bases or amino acids, etc) of the model presented in the Jmol window.

Selecting a molecule so that it’s name heads the menu allows alteration of its appearance in the model.

A molecule can be hidden or revealed using the adjoining checkbox. Hiding a molecule will hide all components (atoms, bonds, ribbon, etc.) of the model associated with that molecule.

Display options

Display options determine how the selected molecule will be rendered in the model. The model may include atoms, bonds, a ribbon, trace, etc, which can be individually sized using the ‘Size’ buttons. The adjoining checkboxes can be used to hide or make visible different model components.

Atoms: Atoms can be rendered as solid spheres with a uniform radius in Angstroms, which together with bonds comprise a traditional ‘ball and stick’ projection. This is normally the default view. Note about hydrogen atoms: some models show hydrogen atoms but others do not.

vdW checkbox: toggles rendering of atoms between uniform diameters and percentage of the van der Waals radius of each element. The van der Waals Radius of an atom is the calculated radius when it is adjacent to but not bonded to another atom. Since the van der Waals radius of an element is related to the size of its electron cloud, elements with greater mass will have larger van der Waals radii.

Dots: This projects an array of small dots around the surface of atoms. Dots are a useful way to show a molecular surface while not obscuring other aspects of the molecular structure, such as a ball and stick rendering. If vdW is checked, the dots are drawn as a percent of the van der Waals radius.

Bonds: Covalent bonds are generally drawn as rods between the atoms. In some models single, double and triple bonds are distinguished (but this does not occur in all models).

H-bonds: The position of hydrogen bonds is calculated by the Jmol applet. This is performed between N-H and C-O groups of proteins and between nitrogenous bases of nucleic acids. Thus, not all hydrogen bonds may be rendered in a model.

Ribbon: A ribbon-like feature that follows the backbone of DNA and proteins. For nucleic acids, a ribbon will follow the sugar-phosphate linkages, and for proteins it follows the path of peptide bonds and alpha carbons. The flattened appearance of the ribbon highlights secondary structural features, such as the alpha-helices and beta-sheets of a protein.

Trace: Like a ribbon, a Trace follows the molecular backbone, but is rope-like in appearance. A Trace shows the path of the backbone while allowing other structural features to be emphasized.

IsoSurface: IsoSurface projects a surface to a molecule as it would appear to water molecules rolling along the perimeter. This is also referred to as the Sovent-excluded or Connolly surface. Follow this link for a more complete description of the rendering of molecular surfaces.

Color by options

Atoms, Ribbons and Traces can be colored to highlight structural features. Follow this link for a more complete description of colors.

Element: Atoms will be colored according to element type. The colors of the most common elements are:

H C N O P S Fe

1o Structure: different types of amino acids and nucleotides are given a unique color (according to the Jmol ‘shapely’ color scheme).

2o Structure: This differentiates regions of protein secondary structure:

α-helix β-sheet

4o Structure: This gives a different color to each peptide subunit of a multi-subunit protein and to each strand of a nucleic acid.



Antigen-binding Proteins of the Immune System

Examine the following models to explore the structure of proteins of the immune system. Feel free to change the appearance of the models as you wish. Instructions for rotating, moving and zooming the models can be found on the MoveModel? link.

1. Antibodies. The options below highlight structural components of a basic immunoglobin structure.

The opening model shows an IgG protein that can be used to show structural components shared by all types of immunoglobins. Select the following options to view these structural features.

Heavy Chain Notice that the two Heavy Chains span the entire molecule, and are associated with the light chains near the antigen binding sites and with each other in the effector region at the bottom of the 'Y'.
Light Chain. The two Light Chains are only part of the antigen-binding regions of the antibody, and contribute to the formation of the antigen binding sites.
Constant region domains. The constant region domains of the light and heavy chains comprise the part of the antibody that is not involved in antigen-binding.
Variable region domains. The domains of the light and heavy chain that form the antigen binding sites are called the variable region, since genetic rearrangements during B-cell development alter the amino acid sequences of the chains.
AG-binding sites. Each antibody monomer possesses two antigen-binding domains at the distal ends of the variable region domains.
Hinge region. In the hinge region the two heavy chains are only loosely associated, allowing for flexibility in the orientation of the antigen binding sites .
Fc.The Fc region is released by a gentle protease treatment that selectively severs the antibody at the hinge region. Note that the Fc region is not equivalent with the constant region.
Fab. The Fab region is also released by gentle protease treatment. Note that the Fab region includes but is not equivalent to the variable region.
Oligosaccharides. Oligosaccharides are attached to the heavy chains, and play in important role in determining the effector functions of the antibody. Antibodies that bind to the same epitope may either trigger or suppress an immune response depending upon the structure of the oligosacharide.
Disulphide bonds. Disulphide bonds form between sulfur atoms of cysteine amino acids. Antibody proteins contain several of these to stabilize the tertiery structure, and in this case, to help hold together a heavy and light chain. Move the molecule to look for other disulphide bonds.

2. Epitopes. The specific molecular site to which an antibody binds is called the epitope. An epitope is said to be linear when it can be defined as a contiguous amino acid sequence. Unlike TCRs, antibodies can also recognize a conformational epitope, i.e., a 3-dimensional antigenic structure created by more than one peptide chain.

Linear epitope. This model shows an antibody Fab fragment bound to a synthetic peptide (colored to show each amino acid) of human angiotensin. The antibody Heavy Chain is colored pink and the Light Chain is blue. The AG-binding region of the antibody is highlighted in spacefill, and a trace along the antigen shows that the epitope consists of a single amino acid sequence.

Conformational epitope. This model shows an antibody Fab fragment bound to lysozyme (colored orange) comprising a conformational epitope. The antibody HC is colored Pink and the LC is Blue. The epitope is highlighted in spacefill, and a trace shows that two peptide loops form the epitope, not a single contiguous sequence of amino scids. Click here to show the lock-and-key association between the epitope and paratope of the antibody (you can move the model during the animation).

3. Polymeric Immunoglobins. Although IgA and IgM occur in monomeric form (similar to the IgG displayed above), secretory IgA is a dimer and secreted IgM is a pentamer.

Dimeric IgA. This particular model displays just the primary sequence of the IgA peptides; i.e., each sphere represents an amino acid. Notice that dimeric IgA are joined at their Fc regions. The J chain is not shown in this model.

Pentameric IgM. As for the previous model, this one displays just the primary sequence of the IgM peptides; i.e., each sphere represents an amino acid. The subunits of pentameric Igm are also joined at their Fc regions. The J chain is shown in this model, and is colored dark red. The immunoglobin used to determine this structure was obtained from a patient with Waldenström's disease, a hyperglobulinemia that commonly produces monoclonal IgM.

3. MHC proteins. MHC proteins present linear peptide epitopes to T-cells receptors.

MHC-II with peptide. This model shows MHC-II presenting a peptide from lysozyme. MHC-II contains an α and a β subunit (projected as ribbons) that contribute to the peptide-binding pocket. In MHC-II the peptide (green) lies relatively flat and sometimes extends beyond the ends of the pocket.

MHC-I with peptide. A model of MHC-I carrying a peptide of the vesicular stomatitis virus. MHC one contains an α subunit and a β-microglobulin peptide, which does not contribute to the peptide binding pocket. The antigenic peptides of MHC-I are generally shorter than those of MHC-II.

4. T-cell receptors -- TCRs. TCRs only recognize linear peptide antigens presented on MHC proteins. The following two models show the extracellular domains of TCRs; the transmembrane regons are not included.

TCR-MHC-II complex. This model shows a T-Cell receptor bound to influenza HA1 antigen presented on MHC-II. The HA1 antigen and MHC-II (DR4) are shown in spacefill; the TCR α and β subunits are shown as ribbons.

TCR-MHC-I complex. This model shows a T-Cell receptor bound to human self-peptide presented on MHC-I. The peptide and MHC-I (DR4) are shown in spacefill; the TCR α and β-microglobulin peptides are shown as ribbons.

5. Other Antigen-binding Proteins. These antigen-binding proteins are part of the innate immune system and bind molecular structures that are broadly distributed among pathogens.

CD1-antigen complex. CD1 comprises a family of proteins that are structurally related to MHC and associated with β-microglobulin and that present non-peptide antigens to specialized T-cells. Here, CD1d holds the glycosphingolipid 'GalA-GSL' of Sphingomonas and a molecule of palmitic acid (possibly to fill and stabilize the binding pocket space).

Toll-Like Receptor (TLR). Approximately a dozen TLRs have been identified with ligands including components of bacterial cell-walls, flagella, and double-stranded RNA. Shown here is the extracellular domain of TLR-3, a glycoprotein, which forms a horse-shoe shaped, solenoid-like structure comprised of 23 leucine-rich repeating units. Click here to show how TLR3 dimerizes when binding double-stranded RNA.

Dept of Biology & Environmental Science

Steven R. Spilatro
© 2008

Test Your Knowledge of Antigen-binding proteins

Answer the following questions and perform the following activities. Change the appearance of the models as necessary to facilitate answering questions.

Name: _______________________

Date: _______________________

Results for Immunology Inquiry Activities

1. Click here to show an antibody molecule. Change the appearance of the model to more clearly show its structural components. Select each structural component listed below, and then click on the corresponding region of immunoglobin model.

a.Click here and then on an Fab.

b.Click here and then on the Fc.

c.Click here and then on a HC domain of the Fab.

d.Click here and then on a constant region domain of a LC.

e.Click here and then on a variable region domain of a HC.

f.Click here and then on the Hinge region.

g.Click here and then on an oligosacchride.

h.Click here and then on a disulphide bond between the two heavy chains.

Attempts: Correct:

2. After selecting each of the models below, change its appearance so that it can be identified.

Model 1 Model 2 Model 3 Model 4 Model 5 Model 6

Find and identify the antigen, if present.
What type of antgen is it?

Carbohydrate Lipid

Identify the type of protein shown in the model.


Attempts: Correct:

3. After selecting each of the Fab models below, change its appearance so that you can determine if it is bound to a linear or a sequential peptide epitope, or non-peptide epitope.

Model 1 Model 2 Model 3 Model 4 Model 5 Model 6

Identify the type of epitope bound by the selected Fab.

Conformational non-peptide

If non-peptide, identify the molecular type of molecule.

Carbohydrate Nucleic acid Lipid

Attempts: Correct: