title: The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A.
abstract: The crystal structure of bovine heart cytochrome c oxidase at 2.8 A resolution with an R value of 19.9 percent reveals 13 subunits, each different from the other, five phosphatidyl ethanolamines, three phosphatidyl glycerols and two cholates, two hemes A, and three copper, one magnesium, and one zinc. Of 3606 amino acid residues in the dimer, 3560 have been converged to a reasonable structure by refinement. A hydrogen-bonded system, including a propionate of a heme A (heme a), part of peptide backbone, and an imidazole ligand of CuA, could provide an electron transfer pathway between CuA and heme a. Two possible proton pathways for pumping, each spanning from the matrix to the cytosolic surfaces, were identified, including hydrogen bonds, internal cavities likely to contain water molecules, and structures that could form hydrogen bonds with small possible conformational change of amino acid side chains. Possible channels for chemical protons to produce H2O, for removing the produced water, and for O2, respectively, were identified.
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Tsukihara
authors.forename: H
authors.initials: H
authors.lastname: Aoyama
authors.forename: E
authors.initials: E
authors.lastname: Yamashita
authors.forename: T
authors.initials: T
authors.lastname: Tomizaki
authors.forename: H
authors.initials: H
authors.lastname: Yamaguchi
authors.forename: K
authors.initials: K
authors.lastname: Shinzawa-Itoh
authors.forename: R
authors.initials: R
authors.lastname: Nakashima
authors.forename: R
authors.initials: R
authors.lastname: Yaono
authors.forename: S
authors.initials: S
authors.lastname: Yoshikawa
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D002467:Cell Nucleus / Q000235:genetics; D003300:Copper / Q000032:analysis; D018360:Crystallography, X-Ray; D004579:Electron Transport; D003576:Electron Transport Complex IV / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006418:Heme / Q000031:analogs & derivatives / Q000032:analysis; D006860:Hydrogen Bonding; D007501:Iron / Q000032:analysis; D008565:Membrane Proteins / Q000737:chemistry; D008929:Mitochondria, Heart / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D008970:Molecular Weight; D009206:Myocardium / Q000201:enzymology; D009711:Nucleotides / Q000378:metabolism; D010084:Oxidation-Reduction; D010100:Oxygen / Q000378:metabolism; D010743:Phospholipids / Q000032:analysis; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017494:Proton Pumps; D014867:Water / Q000378:metabolism
chemical_list: D008565:Membrane Proteins; D009711:Nucleotides; D010743:Phospholipids; D017494:Proton Pumps; D014867:Water; C027728:heme a; D006418:Heme; D003300:Copper; D007501:Iron; D003576:Electron Transport Complex IV; D010100:Oxygen