Note that the first load can be very slow. Be patient until the molecule loads.
(You have have to allow the script to continue if a dialogue tells you that it is too slow.
The loaded molecule is in a view of the contents of a unit cell of the structure of Aarp2 protein in complex
with the RNaseH domain of prp8. Use the mouse to rotate the cell.
Note the axes a, b and c. Look down the b-axis. Note that the a and c axis are skew. The angle between them is β = 108.6 ° ,
given by the values in the top left of the molecule frame. Hit next to find out the asymmetric unit, that is the part of the unit cells
that when operated on by the symmetry of the space group describing the unit cell will recreate the whole unit cell contents.
Note that you can manipulate the view by dragging the mouse as explained here.
Asymmetric Unit
Click the button "Asymmetric Unit" to show the asymmetric unit. The red molecule is RNaseH or prp8 and
the pinkish model is Aarp2.In the following views of other symmetry related molecules, the more primary colour will the RNaseH and the lighter hue will be Aarp2.
We are looking down the b axis (green dot). Note that a is horizontal (red line) and there is a 108.6 ° angle
between it the c axis blue.
The first symmetry operation we shall look at is a two fold rotation about the b axis - that is 180 °
rotation about the green dot, which is a end-on view of the b-axis.
Two Fold Axis
Click the button to see teh two-fold related molecule, in hues of blue.
Note that the blue molecule is related to the red (RNaseH) by a rotation of a half-turn around the green dot,
just as the cyan is to the pink.
Click the button to animate the half-turn rotation, first of the bluish molecules onto the reddish, and then back again.
Two Fold Molecule Translated
The bluish molecules, two-fold related to the reddish, are not in the unit cell draw here.
But they are in the lower right of the next cell, top left, on the other side of the green dot. Because the unit cell describes the repeating pattern of the
crystal by translation alone, we can place where the bluish molecule should come in the original unit cell.
This translated blue molecule will of course we related to another red molecule from the unit cell joining the lower right
of the cell drawn here.
Centring Operation on Asymmetric Unit
The original asymmetric unit (red) is subject to centring in this space group. This translates the molecule half a unit cell along a and c.
Click the button to see this animated.
The yellow-hued molecules are related to the reddish by this centring operation.
Centring Operation on Two-fold related
The two fold related molecule also is subject to centring to create a copy.
Click the button to see this animated.
The green-hued molecules are related to the blue-hued , in the same way as the yellow-hued are to the red-hued
Use the mouse to drag the unit cell around to appreciate the symmetry
Note that the two-fold relations between the differently hued dimers, are at the corners
As we have seen, the red interacts more strongly with the bluish dimer in the cell above to the top-left,
rather than that in its own cell.
Also the yellow interacts in the same way with a green dimer from the unit cell at the top-right
Showing three unit cells
To appreciate the contacts around each unit cell, click the buttons to see three cells along a and c in the ac-plane;
three cells along a and b in the ab plane; and three cells along a,b,c. These calculations may be slow, so be patient if nothing displays for a time.
( You may have to answer a dialogue to allow the script to continue.)
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
Acknowledgement: The format of this
web page is modified from a template provided by Dr. David Marcey,
California Lutheran University , Thousand Oaks, California, USA.