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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