1.2 Pdb  (Page 2/2)

Scroll back up to the top of the summary page. In the blue border on the left of the page click the link entitled "View Structure". Most of the interactive 3D displays require downloading and installing software. For those who do not wish to do this, view the high (500 X 500) resolution ribbons image under "Still Images". This is a ribbons "backbone" model of a protein, that includes the calcium ions, but does not show the sidechains of the individual amino acids. Compare the ribbons model with the cylinders model, wherein all the helices are shown as cylinders. These images are both made with the same atomic coordinates from the 3CLN file, but the coordinates can be modeled in many different ways, depending on what properties the image renderer wants to illustrate.

Now, select the "Download/Display File" option listed in the blue border on the left. For those files that need to be downloaded for making images, usually the text file format is preferred because many of the graphics programs will not accept the html format file. In the table shown under the "Display the Structure File" option, choose the PDB text file format, complete with coordinates. Now, take a look at the contents of the files.

The first column of the PDB file contains an identifier for the type of information contained on that line. For example, JRNL, is the identifier for all lines containing the literary citation(s) for the journal(s) where the structure was published. The first section of the PDB file is the Title Section, which begins with a line containing the identifier HEADER and continues until the end of the lines containing the identifier REMARK. This section includes information about the experimental method used to obtain the atomic coordinates present in the file. The 3CLN structure is an older entry into the PDB, and does not contain a great deal of information about experimental methods and statistics, however newer entries to the PDB are required to have more information. Scroll down until you see the ATOM identifier in the first column. This is the beginning of the atomic coordinates listing and this section of the file should look something like the figure illustrated below.

The 5th column of this file lists the residue number. Notice that in the 3CLN file the first residue number is 5. This is mentioned in the REMARKS section at the beginning of the file, as it should be.

The PDB offers a syntax directory to help interpret the lines and columns in each section of a PDB file. Scroll back to the top of this page and click on the PDB icon in the upper left hand corner to return to the PDB home page. Locate the link entitled "FILE FORMATS". Under PDB File Format, select the most current version of the File Format Contents Guide. Scroll through the Table of Contents listed on the left side of the page. Beginning with the Title Section, links are provided for every possible type of line identifier that can be found within a PDB file. Under the Coordinate Section, click on the link for the line identifier ATOM to call up the Record Format listing for the atomic coordinates section.Each possible field in an item line is listed according to the character column numbers assigned to the field. Not every available field will always be used in a file. For instance, in the Record Format listing, the residue sequence number is listed in the 7th possible field, but the 3CLN file only uses 5 of the first 7 fields and so the residue number is the 5th column. This is because the fields altLoc and chainID are not required in the 3CLN file.

It is common to have more than one structure present in the PDB for a medically or scientifically important protein or nucleic acid, particularly if the structures represent genetically engineered mutants of the same biological molecule, similar molecules from different organisms, or the same molecule bound to different ligands. Return to the PDB home page (the PDB home page icon is always in the upper left hand corner). Enter the accession code 1CFC as a query to the PDB.

Notice that 25 coordinate sets, representing slightly different molecular conformations, are present. This is characteristic of solution studies, where the molecule is dynamic. Use the "View Structure" link to view the ribbons image of a superposition of the 25 models. The parts of the molecule that overlap well between the models are areas that maintain a relatively rigid structure even in solution, while the parts of the molecule that do not overlap well are dynamic in solution. Use the "Download/Display File" link to display the PDB text file, header only, no coordinates.

Before closing this file, view the experimental methods discussed in the Title Section to see how they differ from the 3CLN entry.

Return to the PDB home page and search by keyword calmodulin.

If the query results at the top of the page state that there are structures being processed or "on hold", these listings can be accessed by clicking on the link entitled "matching your query". The Processing/Hold database contains structures that are soon-to-be released. The NIH has a strict release policy, requiring that any structures derived through experiments supported by NIH grants be deposited at the time of submission of a research article to a journal, and although a hold may be placed on these coordinates during the submission process, the rules state that the coordinates are to be released upon publication.