3NBS

Crystal structure of dimeric cytochrome c from horse heart

Summary for 3NBS

• Entry DOI: 10.2210/pdb3nbs/pdb
• Related: 3NBT
• Descriptor: Cytochrome c, HEME C, TETRAETHYLENE GLYCOL, ... (6 entities in total)
• Functional Keywords: cytochrome c, polymerization, domain swapping, electron transport
• Biological source: Equus caballus (domestic horse,equine)
• Total number of polymer chains: 4
• Total formula weight: 50167.04

Authors

Taketa, M.,Komori, H.,Hirota, S.,Higuchi, Y. (deposition date: 2010-06-04, release date: 2010-07-14, Last modification date: 2024-10-16)

Primary citation

Hirota, S.,Hattori, Y.,Nagao, S.,Taketa, M.,Komori, H.,Kamikubo, H.,Wang, Z.,Takahashi, I.,Negi, S.,Sugiura, Y.,Kataoka, M.,Higuchi, Y.
Cytochrome c polymerization by successive domain swapping at the C-terminal helix
Proc.Natl.Acad.Sci.USA, 107:12854-12859, 2010

PubMed Abstract: Cytochrome c (cyt c) is a stable protein that functions in a monomeric state as an electron donor for cytochrome c oxidase. It is also released to the cytosol when permeabilization of the mitochondrial outer membrane occurs at the early stage of apoptosis. For nearly half a century, it has been known that cyt c forms polymers, but the polymerization mechanism remains unknown. We found that cyt c forms polymers by successive domain swapping, where the C-terminal helix is displaced from its original position in the monomer and Met-heme coordination is perturbed significantly. In the crystal structures of dimeric and trimeric cyt c, the C-terminal helices are replaced by the corresponding domain of other cyt c molecules and Met80 is dissociated from the heme. The solution structures of dimeric, trimeric, and tetrameric cyt c were linear based on small-angle X-ray scattering measurements, where the trimeric linear structure shifted toward the cyclic structure by addition of PEG and (NH(4))(2)HPO(4). The absorption and CD spectra of high-order oligomers (approximately 40 mer) were similar to those of dimeric and trimeric cyt c but different from those of monomeric cyt c. For dimeric, trimeric, and tetrameric cyt c, the DeltaH of the oligomer dissociation to monomers was estimated to be about -20 kcal/mol per protomer unit, where Met-heme coordination appears to contribute largely to DeltaH. The present results suggest that cyt c polymerization occurs by successive domain swapping, which may be a common mechanism of protein polymerization.

PubMed: 20615990
DOI: 10.1073/pnas.1001839107

Experimental method

X-RAY DIFFRACTION (2.2 Å)