homework#3

1. Find the structure of prion from PDB. (A) List the following
information : (1)
ID number, (2) Authors, (3) The number of residues in one monomer, (4) The number of disulfide bonds.(B) Put the structure of prion on your homepages. Show different color for different secondary structure in cartoon form with sidechains on1. Find the structure of prion from PDB. (A) List the following information : (1) ID number, (2) Authors, (3) The number of residues in one monomer, (4) The number of disulfide bonds. (B) Put the structure of prion on your homepages. Show different color for different secondary structure in cartoon form with sidechains on (helix in blue, sheets in red). Show the script that makes the final picture.

ANSWER:

   A. (1) ID number:  

                1AG2

             (2) Authors:

                 M.BILLETER                    R.RIEK

                 G.WIDER                          K.WUTHRICH

                 S.HORNEMANN             R.GLOCKSHUBER

            (3) How many residues in one monomer:

                  103  residues

             (4) The number of disulfide bonds:

                 There is only one SSBOND between CYS 179 and CYS 214

B.

script

2. Transcription of the ant gene during lytic growth of bacteriophage P22 is regulated by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Please find the
co-crystal structure of this Arc tetramer-operator complex from PDB.
(a) Make an animation (by Gifbuilder) of whole complex.
(b) Show the DNA sequences of the Arc operator.
(c) The picture below is the hydrogen bonds between beta-sheet side chains and DNA bases. Show three side chains (gln9, asn11, arg13) from one monomer and corresponding DNA bases of them on your homepage. Color three side chain with different color. Measure the distance between possible hydrogen bonds.

hw3.jpg (24224 bytes)

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ANSWER:

A.

arc.gif (23609 bytes)

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B.

        5'   T A T A G T A G A G T G C T T C T A T C A T

     3'   A A T G A T A G A A G C A C T C T A C T A T

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C.

arehb.gif (6295 bytes)