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Exact(6)
All these structures show the intact structure of CI to be L-shaped, with a matrix arm and a membrane arm.
Likewise, the bridge-like structure formed by domains 5 and 6 of the matrix arm and the proximal/central membrane protuberance (PMP/CMP) on the membrane arm (Clason et al, 2010) was present only in the eukaryotic enzyme.
The bridge-like connection formed by the complex I domains 5/6 on the matrix arm and the PMP/CMP on the membrane arm appears thicker in the supercomplex than in the isolated complex I (Clason et al, 2010).
The 6-Å map of complex I from Y. lipolytica (Hunte et al, 2010) (provided by Carola Hunte, Universität Freiburg) was fitted to the clear features of the matrix arm and on the intermembrane side in the supercomplex map.
The regions not occupied by bacterial complex I included the intermembrane protuberance 2 (IP2) on the intermembrane side of the matrix arm and the distal membrane protuberance (DMP) on the distal end of the membrane arm on the matrix side (Clason et al, 2010).
All ND subunits are located in the membrane-bound portion of the NADH dehydrogenase complex; ND1 is thought to be located at the junction between the matrix arm and membrane-embedded arm, and ND2 and ND5 are located in the membrane-embedded arm where proton pumping occurs [ 40].
Similar(54)
When compared with CI in the free form, the matrix arm of CI and the distal end of CI's membrane arm bend a little towards the central part of CI's membrane arm in the respirasome, to better interact with CIII and CIV.
To account for the different angle between matrix and membrane arm in the supercomplex as compared with T. thermophilus (PDB 3M9S; Efremov et al, 2010), the matrix arm from T. thermophilus (PDB 3IAM; Sazanov and Hinchliffe, 2006) and the membrane arm from Escherichia coli (PDB 3M9C; Efremov et al, 2010) were fitted separately.
The CIII dimer has a two-fold axis, which is perpendicular to the membrane plane, with the matrix domains of CIII protruding around 75 Å out of the membrane and facing the matrix arm of CI.
The matrix arm containing NDUFV1, NDUFV2, NDUFS1, NDUFS2, NDUFS3, NDUFS7 and NDUFS8 accommodates FMN molecule and the Fe-S clusters, which oxidizes NADH and transfers electrons to the Q reaction site.
Eventually, a volume with clear structural features for the matrix arm of complex I with its subdomains, and the matrix domains of complex III, was chosen as the initial model.
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