Rop Protein Dimer

Select & Highlight:
"a-positions"
"d-positions"

Heptad units:
1 2 3
4 5 6
7 8
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Rotate:
X 90° X -90°
Y 90° Y -90°
Distances:
Length
(in Å units).
Width
(in Å units).
Reset

Highlight the residues that are the same or different in the Janus protein of Dalal, S., et al. (1997) "Protein alchemy: Changing b-sheet into a-helix"Nature Struct. Biol.7, 548. Consult their Fig. 1c for details.

The positions in Janus that are identical in Rop are colored red.

The positions in Janus that are identical in Protein G are colored light blue.

The positions in Janus that are identical in Rop and Protein G are colored green.
(All other residues retain their original colors.)
View a helical wheel diagram of Rop protein in a pop-up window. The diagram is a useful complement to the Chime image and vice versa.
Rop Protein DimerOverall Architecture of the Rop Protein Dimer.
The starting display of this four-helix bundle protein is wireframe with a backbone trace. The A subunit of the homodimer is colored white; the B subunit is colored cyan. The amino- and carboxyl-termini of each chain are labeled.
Viewing Suggestions:
1. The "Select & Highlight" buttons color the "a-position" sidechains green and the "d-position" sidechains pink. Together, these residues make up the hydrophobic core of the structure. (Each button also leaves the image with the corresponding sidechains selected; thus, alternative color or display choices can be chosen for each group from the Chime menu.)
2. The "Heptad units" buttons highlight consecutive seven-amino acid segments of chain B and label the a-postion and d-postion amino acids in each group. After highlighting a unit, choose Spacefill and CPK from the Chime menu to see how each pair of amino acids packs against the sidechains of chain A.
3. The rotate buttons act on the entire structure. Remove the distance monitors with a second click.
4. After highlighting the core residues, view the structure end-on; then slab through the length of the four-helix bundle to see the packing of the highlighted side chains. (Select Slab Mode in the Chime Options menu and hold the control key down while dragging the mouse vertically in the image.)
The dimer shown here is the "Biological functional unit" derived from the monomer coordinates (1rop.pdb).
Banner, D. W. et al. (1987) "Structure of the ColE1 rop protein at 1.7 Å resolution"J. Mol. Biol.196, 657.
The boxed area below contains a RasMol script that will produce the starting display on this page; it then highlights the a-position and d-postion residues sequentially. (Select and copy the text in the box for viewing in RasMol.)

# The script used to display the starting view and highlighted residues: #!rasmol -script # File: RopDimer.spt on 1ropbio.pdb # Creator: RasMol Version 2.6 # W. McClure 9/16/98 # Load the Rop Dimer file into RasMol; # Then call this script. background [0,0,0] set ambient 60 set specular off reset slab off rotate z 78 rotate y 20 rotate x -25 set bonds off set axes off set boundingbox off set unitcell off set hbond sidechain set bondmode and dots off # Avoid Colour Problems! select all colour bonds none colour backbone none colour hbonds none colour ssbonds none colour ribbons none colour white trace 60 # color chain A, white and chain B, cyan select *:a color white select *:b color cyan select 1 and alpha label "N" select 56 and alpha label "C" color labels yellow set fontsize 9 echo " Dimer of Rop Protein" echo " Wireframe display with backbone trace." echo " Chain A is colored white." echo " Chain B is colored cyan." echo " The N- and C-termini are labeled." echo " " echo " Press SPACE to highlight the 'a' positions." echo " " pause # color the a positions, green and spacefill select 5,12,19,26,31,38,45,52 define apos selected select apos and (sidechain or alpha) spacefill color green echo " The 'a' positions on each chain are highlighted." echo " Spacefill display; colored green" echo " (defined as, 'apos')" echo " " echo " Press SPACE to highlight the 'd' positions." echo " " pause # color the d positions, red and spacefill select 8,15,22,29,34,41,48,56 define dpos selected select dpos and (sidechain or alpha) spacefill color red echo " The 'd' positions on each chain are highlighted." echo " Spacefill display; colored red" echo " (defined as, 'dpos')" echo " " echo " Press SPACE to finish." echo " " pause select all echo " Viewing suggestions:" echo " View the structure end-on and slab down the length." echo " Label the highlighted residues at their beta carbons." echo " eg. 'select apos and *.cb' then 'label %m%r'." echo " "