Cytochrome Oxidase
PDB file 1OCC
This structure of mammalian cytochrome oxidase (complex IV) was determined by Tsukihara et al., in 1996. There are 2 identical complexes, each including 13 different polypeptides and 6 metal centers (hemes a & a3, CuA, CuB, Mg, & Zn).
Suggested display options:
1. Structure within the membrane.
Color chain, and display as cartoon.
Look for the intramembrane domains, with transmembrane a-helices perpendicular to the plane of the membrane.
Select hetero-ligand, and
display as spacefill
with color CPK.
Zoom in (hold down shift key and drag).
Question: What is the
orientation of the hemes relative to the membrane?
2. Metal centers.
Make
the protein disappear: select protein, and then select hide.
If metal centers are not visible,
select ligand,
color CPK,
& display spacefill.
Identify the binuclear center (CuB & heme a3),
heme a, and CuA (2 Cu close together).
It might help to select and change the color of zinc to distinguish from copper. (Zinc atoms have only
a structural role.)
3. Ligands to metal centers.
With the protein invisible and ligands displayed as above, select the following residues, color CPK, and display as ball & stick (n or o refer to specific proteins of the complex): Select his61n, his378n, his376n,
his240n, his290n, his291n, his161o, his204o, cys196o, cys200o, met207o, glu198o.
Question: How do the ligands of heme a and a3
differ?
Select all, and
then select hide,
to make
everything disappear.
Now select 515n (heme
a) and display as spacefill or ball &
stick.
Select 50-85n, 371-395n and display
as ribbon.
Right
drag with the control key held down to center the heme in the window.
Select his61n, his378n and
display as sticks or ball & stick, with
color CPK.
Questions:
How is heme a is held in place within the
membrane?
How
does this explain the orientation of the heme plane relative to the
membrane bilayer?
Identify the
farnesyl side-chain (3
isoprenoid units) of heme a. (Compare to diagram
of heme a.)
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Lecture Notes
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