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. 2023 Sep 23;14:5942. doi: 10.1038/s41467-023-41640-9

Fig. 3. Substrate engagement in the active Pex1/Pex6 D2 channel.

Fig. 3

a Top view of the substrate-bound Pex1/Pex6 D2 ring. Pex1(D1) (coral), Pex6(D2) purple, ISS motif (cyan), nucleotides (green) and substrate (yellow). The insets show magnified images of the ATP binding sites at the Pex1(D2)-Pex6(D2) (upper image) and Pex6 (D2)-Pex1(D2) interface (lower image) of substrate engaged subunits C and D. b Residues of pore loops 1 contacting the substrate. c Multiple alignments of pore loop 1 sequences of D2 domains from several AAA-ATPases including Pex1, Pex6, Rix7, p97/Cdc48, AFG3L2 and ATAD1. d Pex1 and Pex6 subunits shown side-by-side, aligned along their D1 domain. Note the sequential tilt of the D2 domain relative to the D1, which is highlighted by a dashed line above each domain. The catalytically “dead” D1 domains remain ATP-bound. e Spiral arrangement of pore loops 2. Pore loops 1 are shown in grey and substrate in yellow. The pore loops 2 of subunits Pex1(A) to Pex6(E) (PL2) form a second spiral staircase running below and parallel to the spiral staircase formed by the pore loops 1 (PL1). The pore loops of the “seam” subunit Pex6(F) (highlighted in gray) are displaced significantly from the spiral staircase.