Slide 1 My name is Yoshitaka AISU. E-mail address: (withheld) Professor of my laboratory is Takahisa IKEGAMI. My research project is not already decided. But, I will research the structure of any proteins by NMR The name of my protein is ADP-ribosylation factor 6 (ARF6) and its function is cell invasion. PDB code is 2D1X. Resolution is 1.90Å, R-Value 0.216, and R-free 0.226. This report is made available with the kind permission of the student who prepared it, Yoshitaka Aisu. It was prepared for the 2010 class at Osaka University, Japan (workshops.molviz.org). The only change is that the student’s email address was removed, and this paragraph was added. Each slide answers a specific question.

Slide 2 six protein chains, no DNA, no RNA.

Slide 3 Ligands Three letter codes SO4 Full name SULFATE ION

Slide 4A only beta sheet there is no disulfide bond.

Slide 4B 3KJ6 2 disulfide bonds within chain L 2 disulfide bonds within chain H 2 disulfide bonds between chain L and chain H

Slide 5 There is a hydrophobic core.

Slide 6 This protein is soluble .

salt bridge and hydrogen bond Slide 7 salt bridge and hydrogen bond

Slide 8 High conserved GLU21:A - expected Because GLU21 is near the legand SO4. High conserved VAL57:A - unexpected

conformation is difference between the AU and PISA. Slide 9 Asymmetric unit Biological unit PISA 6 chains 6 chains conformation is difference between the AU and PISA. Author’s biological unit is 3 chains.

Slide 10 List the gap in 2D1X chain A : 1-6 chain P : 1-2 chain P : 12-15 chain B : 1-7 chain Q : 1-2 chain Q : 12-15 chain D : 1-7

Slide 11 Sandbox Reserved 3 change colors

Slide 12 red: negative charge blue: positive charge

Slide 13 Number of energetically significant ARG/TYR cation-pi interactions: 2 ARG42:A with TYR49:C ARG4:Q with TYR12:D

Slide 14 Residue of high temperature Glu1:C

Thank you for your lecture. I enjoy leaning computer science. See you , again.