Example images

The example images are all based on the structure of the Ras p21 protein (Ras, for short) determined by NMR spectroscopy (Kraulis et al 1994). For simplicity, the hydrogen atoms have been stripped from the coordinate file, which is called ras.pdb in all example input files. All example input files are available in the distribution directory molscript/examples.

General example images
VRML example images
MolAuto example images
The Ras p21 protein
The Ras p21 structure

General example images

Image (small JPEG)	In other formats	Input file
	PostScript Raster3D (SGI) Raster3D (JPEG) VRML 2.0 VRML 2.0 gzipped EPS SGI JPEG (large) PNG GIF	ras_std.in The secondary structure colouring is the default from MolAuto.
	PostScript Raster3D (SGI) Raster3D (JPEG) VRML 2.0 SGI JPEG (large)	ras_rmsd.in The same as above, but with colouring according to RMSD of the atoms, by setting the residuecolour... b-factor and colourparts parameters. Notice that the colours vary over the secondary structure elements.
	VRML 2.0 SGI JPEG (large) PNG	ras_shiny.in The secondary structure colouring is the default from MolAuto. The specularcolour parameter has been set to white, and the shininess of the atoms increased to 0.6.
	PostScript VRML 2.0 VRML 2.0 gzipped JPEG (large) GIF	ras_cyl.in Cylinders for helices, and colouring according to secondary structure type; highlighting loops involved in ligand binding and conformational variability.
	Raster3D (SGI) Raster3D (JPEG) VRML 2.0 VRML 2.0 gzipped JPEG (large)	ras_gdp.in Closeup of the GDP molecule and some interacting residues. Some labels are shown and some interactions are shown schematically.

VRML example images

A set of VRML files and HTML text organized into frames show some possibilities of how to use VRML for description of protein structures, involving anchors. Also an example showing the use of the level-of-detail (LOD) construct.

Ras VRML files organized in frames.
Ras VRML files in non-frames organization.
Ras VRML level-of-detail (LOD) example (gzipped) showing the use of the level-of-detail command.

MolAuto example images

These images were generated directly from the PDB data set via the MolAuto program, which produces first-approximation input files from a PDB file. It should be noted that the view orientation is not very good; MolAuto does not transform the coordinates in any way.

Command-line options Image (small JPEG) Files

[none: default] molauto PostScript
VRML 2.0
VRML 2.0 gzipped
JPEG (large)

-nice -cpk molauto nice PostScript
VRML 2.0
VRML 2.0 gzipped
JPEG (large)

Command-line options	Image (small JPEG)	Files
[none: default]		PostScript VRML 2.0 VRML 2.0 gzipped JPEG (large)
-nice -cpk		PostScript VRML 2.0 VRML 2.0 gzipped JPEG (large)

The Ras p21 protein

The Ras p21 protein is a central component in the cell-signalling system that transmits extra-cellular growth signals via cell membrane receptors, via a cascade of signalling molecules into the nucleus. It is present in many cell types, and several forms of cancer are associated with a mutated form of the protein, where it is locked in a growth-promoting state.

Ras p21 is an enzyme; it hydrolyzes GTP (guanosine triphosphate) to GDP (guanosine diphosphate); it is a GTPase. The protein exists in vivo as a ternary complex with one magnesium ion (Mg) and GDP (or GTP).

The function of Ras is to act as a molecular switch with two possible states, on or off. In the GTP-bound form it is active, and binds to certain other proteins called effectors. The effectors transmit the growth signal further down the signal transduction cascade. This is how Ras p21 transmits the growth signal to the rest of the molecular machinery in the cell.

The signal is switched off by hydrolysis of the GTP to GDP. Ras is fairly inefficient as an enzyme in itself, but its catalytic rate is considerably enhanced by interaction with certain other proteins, such as Ras-GAP (GTPase Activating Protein). Other molecules are responsible for activating Ras by promoting exchange of the GDP molecule for a GTP molecule, as a response to extra-cellular signals.

In many of the cancer-associated mutants of the Ras p21 protein, the ability to hydrolyse GTP is impaired. The active GTP form of the protein is therefore not converted into the inactive GDP form as fast as it should, so the growth signal is transmitted for too long. This contributes to the uncontrolled cellular growth which is characteristic of tumours.

The Ras p21 protein is also the prototypical representative for a large class of signalling proteins called the small GTPases. Other proteins in this family are Rho and Rab.

The Ras p21 structure

The 3D structure of Ras p21 used in these example images was determined by heteronuclear multidimensional NMR spectroscopy, as described in:

Kraulis P.J., Domaille P.J., Campbell-Burk S.L., Van Aken T., & Laue E.D.
Solution structure and dynamics of Ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy.
Biochemistry (1994) vol 33, pp 3515-3531.

Here is the PubMed entry giving the abstract of this paper.

The Protein Data Bank (PDB) code for the coordinate set used here is 1CRQ, stripped of all hydrogen atoms. This contains the minimized average structure. The 40 individual structures are available in two separate PDB data sets with 20 structures each: 1CRR and 1CRP.

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