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. 2021 Apr 30;9:672851. doi: 10.3389/fchem.2021.672851

Figure 2.

Figure 2

Q binding positions. (A) The Q reduction site in the peripheral arm of complex I (PDB: 6RFR) is formed by subunits NDUFS2 (green) and NDUFS7 (blue). A tunnel for Q access from the membrane traverses subunit ND1 (pink). The tunnel was calculated using the CAVER3 software (Chovancova et al., 2012) (starting point conserved Y144, PDB: 6RFR, probe radius 1.3 Å). Intermediate Q binding positions determined by computational methods are indicated by Arabic numbers according to Haapanen et al. (2019). The positions of Q molecules (head group) modeled into X-ray or cryo-EM structures are indicated by Roman numbers and are shown in detailed views in separate panels; the direction of view is consistent for panels in the same row. (B) DBQ bound to complex I from T. thermophilus (PDB: 6I0D) (Y, Y87; H, H38); (C) DBQ bound to complex I from Ovis aries in the closed state during turnover (PDB: 6ZKC) (Y, Y108; H, H59); (D) PL9 bound to ndh complex I from T. elongatus BP-1 (PDB: 6KHJ) (Y, Y72; H, H23; A, A237; R3, R329); (E) Q9 bound to complex I from Y. lipolytica (PDB: 6RFR) (R1, R27; R2, R108, R3, R297; F, F228); (F) DBQ bound to complex I from O. aries in the closed state during turnover (PDB: 6ZKC) (R1, R25; R2, R77, R3, R274; F, F224); (G) DBQ bound to complex I from O. aries in the open state with NADH bound in the N module (PDB 6ZKH) (R1, R25; R2, R77, R3, R274; F, F224); (H) DBQ bound to complex I from O. aries in the open state during turnover (PDB 6ZKD) (R1, R25; R2, R77, R3, R274; F, F224).