HOMEWORK#3

Viewing Proteins / PDB

1. Find the structure of prion from PDB, then list the following information : (1) ID number, (2) Authors, (3) The number of residues in one monomer, (4) The number of disulfide bonds. ,(5) The structure of prion

(1) ID number :

(2) Authors :

  • M.BILLETER,R.RIEK,G.WIDER,K.WUTHRICH,S.HORNEMANN,R.GLOCKSHUBER

(3) The number of residues in one monomer :

  • from Gly124 to Tyr226

(4) The number of disulfide bonds :

  • one disulfide bond at residues Cys179-Cys214

(5) The structure of prion :

 

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.

  • Chain E: Nucleic acid sequence ( 22 bases )
    • Sequence: T-A-T-A-G-T-A-G-A-G-T-G-C-T-T-C-T-A-T -C-A-T

  • Chain F: Nucleic acid sequence ( 22 bases )
    • Sequence: A-A-T-G-A-T-A-G-A-A-G-C-A-C-T-C-T-A-C -T-A-T

(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 home page. Color three side chain with different color. Measure the distance between possible hydrogen bonds.

Gln 9D - A7F Asn 11D - T17E Arg 13D - G4F

 

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