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1 BUILDING A STRUCTURAL MODEL OF KCSA 8

Coordinates ﬁle. The ﬁle 1K4C.pdb corresponds to the X-ray struc-

ture of KcsA reﬁned at 2.0

A resolution provided by Yufeng Zhou,

Jo˜ao H. Morais-Cabral, Amelia Kaufman, and Roderick MacKin-

non, Nature 414, 43–48 (2001). Dr. MacKinnon received the 2003

Nob el Prize in Chemistry for discoveries concerning channels in cell

membranes.

1.2 Examining the PDB File

PDB ﬁles are simply text ﬁles, and contain more information than just atomic

coordinates. Here we will look at the ﬁle you downloaded in a text editor and

examine its contents.

1 Open the the ﬁle 1K4C.pdb in your favorite text editor, e.g. by typing

emacs 1K4C.pdb in a terminal window.

2 First, simply look through the ﬁle. Notice the plethora of information:

authors, resolution, experimental method, secondary structure, etc. The

atomic coordinates don’t start until line 577!

3 Now we will look at some speciﬁc parts which are particularly important.

First, look at the COMPND items beginning on line 4.

COMPND MOL_ID: 1;

COMPND 2 MOLECULE: ANTIBODY FAB FRAGMENT HEAVY CHAIN;

COMPND 3 CHAIN: A;

COMPND 4 MOL_ID: 2;

COMPND 5 MOLECULE: ANTIBODY FAB FRAGMENT LIGHT CHAIN;

COMPND 6 CHAIN: B;

COMPND 7 MOL_ID: 3;

COMPND 8 MOLECULE: POTASSIUM CHANNEL KCSA;

COMPND 9 CHAIN: C;

COMPND 10 FRAGMENT: POTASSIUM CHANNEL KCSA;

COMPND 11 ENGINEERED: YES;

COMPND 12 MUTATION: YES

These items list the protein chains which you looked at above (Fig. 2). We

see that chain C is the KcsA channel we are interested in. In addition to those

listed here, there is a chain X which contains the water molecules, ions, and

lipid fragments.

4 We want to build a system with a whole KcsA channel, a tetramer, yet the

PDB ﬁle we have downloaded contains only one monomer. To generate the

missing subunits, we must apply transformation matrices. These matrices

are given in REMARK 350 of the PDB ﬁle. Find this section.

1 2 3 4 5 6 7 8 9 10 11 12 13 ... 42 43

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SanDisk Membrain Software Manual de usuario Pagina 8