4HEA

Author Information : The coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 4HE8 (membrane domain) and 4HEA (entire complex).

The models for each complex were derived from the following X-ray crystallographic data; Complex I (NADH dehydrogenase) 4HEA and 3M9S [2] , [70] , Thermus thermophilus ; II (succinate dehydrogenase) 1... OY [71] ; Sus scrofa , III (cytochrome bc 1 ) 1BE3 [8] , Bos taurus ; IV (cytochrome c oxidase) 1OCC [72] , Bos taurus ; V (ATP synthase) 1C17 [73] , Escherichia coli and 1H8E, Bos Taurus [74] .

PDB ID 4HEA.

( B ) Complex I of the electron transport chain has an unusually large number of highly co-varying inter residue pairs not in contact in the crystal structure of 4HEA; these contacts may be formed in ... ifferent state of the complex.

Comparison of the X-ray structure of NDH-1 from T. thermophiles [6] (PDB code: 4HEA) to the electron density map from NDH-1L that was retrieved in this study was done by using UCSF Chimera [29] and Ad... be Photoshop.

Extended Data Fig. 5 Comparison of the individual structures of the core subunits of bacterial and mammalian complex I a) The structure of each subunit from T. thermophilus (wheat, 4HEA.

Baradaran R , Berrisford J.M , Minhas G.S , Sazanov L.A , 2012 , Crystal structure of the entire respiratory complex I from Thermus thermophilus , 4HEA ; http://dx.doi.org/10.2210/pdb4HEA/pdb , Public... y available at the RCSB Protein Data Bank.

( c ) Overlay of X-ray electron density map (gray surface, contour level 1.9) with an EM envelope of Yarrowia lipolytica complex I (gray mesh) and the X-ray structure of bacterial Thermus thermophilus... complex I (PDB file 4HEA); central subunits: NDUFS2 subunit (NQO4, blue; N-terminal β-sheet highlighted in yellow), NDUFS7 subunit (NQO6, cyan), NDUFS8 subunit (NQO9, orange), NDUFS3 subunit (NQO5, hot pink), loop connecting helices 1 and 2 of subunit ND3 (NQO7, red); structure of ACP from E. coli (PDB file 2FAE, pink; decanoyl phosphopantetheine, yellow stick representation) fitted to electron density (magenta); please compare the original figure of the publication [ 25 ].

Structural Analysis Protein Data Bank (PDB) files 2YBB (supercomplex of I, III, and IV), 4HEA (complex I), 1PPJ (complex III), 1V54 (complex IV), and 1E79 with 1C17 (complex V) were rendered and color... d with the Visual Molecular Dynamics viewer 1.9.1 ( Humphrey et al. 1996 ).

We inferred the potential function of positively selected amino acid sites belonging to MT-ND subunits by mapping them onto the 3D crystal structure of Thermus thermophiles (PDB ID: 4HEA), a Gram nega... ive eubacterium [ 56 ].