Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology

Abstract

SummaryWe determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 of the 60 dimer subunits. Horizontal helices of subunit a in Fo wrap around the c-ring rotor, and a total of six vertical helices assigned to subunits a, b, f, i, and 8 span the membrane. Subunit 8 (A6L in human) is an evolutionary derivative of the bacterial b subunit. On the lumenal membrane surface, subunit f establishes direct contact between the two monomers. Comparison with a cryo-EM map of the F1Fo monomer identifies subunits e and g at the lateral dimer interface. They do not form dimer contacts but enable dimer formation by inducing a strong membrane curvature of ∼100°. Our structure explains the structural basis of cristae formation in mitochondria, a landmark signature of eukaryotic cell morphology.

Structure and function of the intermembrane space domain of mammalian FoF1ATP synthase

“…Accordingly, DAPIT accounts for the elongated tubular sub-domain of the IMD, while 6.8PL occupies the globular sub-domain, anchoring the IMD to the remainder of F o ( Figure 2D). We then examined if this model is in line with our own and a recent crosslinking study [30] focusing on the unassigned bovine [20] and the ciliate P. tetraurelia [25] ( Figure 4). In all these ATP synthases, a structural feature -like the bovine IMD -extends on the intermembrane side from the rotor distal part of F o towards the rotor ring suggesting that an IMD is a common feature of diverse mitochondrial ATP synthases.…”

“…forms b-e-g complex present in early DDM/column extracts in absence of lipids [28] cryo-EM [16] null-mutants and cryo-EM studies of yeast enzyme [8,20] knock-down in human enzyme [10] cross-linking [29,30], [present study] assembly study [31] f low tight association with Fo retained in IMD and Fo kink-less subcomplex structures in yeast vicinity to b, A6L, e, g and 6.8PL…”

“…N-terminus exposed to matrix present in early DDM/column extracts in absence of lipids [28] cryo-EM [20] cross-linking [29,30] proteolysis [29] g low tight association with Fo retained in IMD less cryo-EM structure exhibiting Fo kink thought to cause membrane bending (Fo kink) in neighborhood to b, e, f N-terminus exposed to matrix forms b-e-g complex present in early DDM/column extracts in absence of lipids [28] cryo-EM [16] null-mutants and cryo-EM studies of yeast enzyme [8,20] knock-down in human enzyme [10] cross-linking [29], [present study]…”

“…As a consequence, only crystal structures of stable sub-complexes are available, encompassing the membrane-extrinsic F 1 domain, and the rotor-ring (c-ring) of the transmembrane F o part [4,[12][13][14][15]. These structures provided important insights into the core function of ATP synthesis, while cryo-EM studies provided first lower-resolution structures of the intact complex [16][17][18][19][20].…”

“…The latter two subunits, 6.8PL and DAPIT, were only lately recognized as regular subunits due to their weak association with the complex [21][22][23][24]. Very recently, a novel domain on the intermembrane space side of mitochondrial F o F 1 ATP synthase has been visualized in cryo-EM studies from diverse organisms: in the bovine monomeric ATP synthase complex [18,19], as well as in the dimeric complexes of the yeast Yarrowia lipolytica [20] and the ciliate Paramecium tetraurelia [25]. The domain is only poorly defined in the bovine ATP synthase structures and the identity of the comprising subunits is unknown.…”