PDBsum entry 3cxh

Oxidoreductase

PDB id: 3cxh

Contents

Protein chains

431 a.a.

352 a.a.

385 a.a.

246 a.a.

185 a.a.

74 a.a.

125 a.a.

93 a.a.

55 a.a.

127 a.a.

107 a.a.

112 a.a.

Ligands

GLC-FRU

UMQ ×2

HEM ×7

SMA ×2

8PE ×2

CN6 ×2

9PE ×2

7PH ×2

FES ×2

6PH ×2

Waters ×548

References listed in PDB file

Key reference

Title

Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer.

Authors

S.R.Solmaz, C.Hunte.

Ref.

J Biol Chem, 2008, 283, 17542-17549. [DOI no: 10.1074/jbc.M710126200]

PubMed id

18390544

Abstract

In cellular respiration, cytochrome c transfers electrons from cytochrome bc(1) complex (complex III) to cytochrome c oxidase by transiently binding to the membrane proteins. Here, we report the structure of isoform-1 cytochrome c bound to cytochrome bc(1) complex at 1.9 A resolution in reduced state. The dimer structure is asymmetric. Monovalent cytochrome c binding is correlated with conformational changes of the Rieske head domain and subunit QCR6p and with a higher number of interfacial water molecules bound to cytochrome c(1). Pronounced hydration and a "mobility mismatch" at the interface with disordered charged residues on the cytochrome c side are favorable for transient binding. Within the hydrophobic interface, a minimal core was identified by comparison with the novel structure of the complex with bound isoform-2 cytochrome c. Four core interactions encircle the heme cofactors surrounded by variable interactions. The core interface may be a feature to gain specificity for formation of the reactive complex.

Figure 2.
FIGURE 2. The interface of cyt c (green) and cyt c[1] (pink) at high resolution. Hemes, black; water molecules, cyan. A, 2F[o] - F[c] electron density map at the interface, contoured at 1 and drawn as a blue mesh. B, stereo view of the core interface. The minimal core interface (dashed lines) is defined by four residue pairs (labeled) that were identified in three structures of the electron transfer complex. The contact of the heme CBC atoms is shown as a dotted line.

Figure 3.
FIGURE 3. The building blocks of the interface. The cyt c[1] (A)-cyt c (B) interface is shown in open book view. The heme groups (black) are encircled by the core interface (orange area, interacting atoms as orange spheres). The variable interface (yellow) surrounds the latter. Residues mediating long-range electrostatic interactions (pink and blue for negative and positive charges, respectively) form a semicircle around the central hydrophobic contact site. C, the semitransparent surface representation of cyt c[1] (gray) and cyt c (green) shows the position of these long-range electrostatic interactions in the high resolution structure (Table 1) as highlighted in blue-green and pink (positive and negative charges, respectively). Heme groups are shown in black. A high number of water molecules (cyan spheres) are bound at the interface of cyt c[1] (D) but not of cyt c (E). Only two of these water molecules form hydrogen bonds to both cyt c[1] and cyt c (green spheres). F, interface water molecules bound to cyt c[1] colored in cyan and green (as in D) are superimposed with all surface water molecules that are present at the other cyt c[1] with the non-occupied cyt c binding site (dark blue spheres). Surface water molecules up to a distance of 3.5 Å are included.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 17542-17549) copyright 2008.