Figure 3. Comparison between the locked and unlocked monomer.
(A) Locked (right) and flexible, unlocked monomer (left). Atomic B-factors are shown using the indicated color coding. The inset shows the crystal contacts acting on PsbU in the right monomer. (B) A slice through the unlocked PSII monomer showing D1 and extrinsic, manganese stabilizing subunits PsbU, PsbV, PsbO (the 147–193 loop and the position of the external β-barrel). The inset shows the WOC-binding site and C-terminal loops of both PsbU and D1 including, residues involved in their interaction (Tyr103 and Pro340) and residues involved in cluster binding in intact PSII.
Figure 3—figure supplement 1. Overlay of Cα atoms (spheres) of D1 residues between the WOC site and the acceptor site (Fe, QA, QB).
The present structure is shown in green, the reference structure from the same crystal system but not treated with NH2OH and EDTA (PDB: 4PJ0) is shown in blue. D1 Helices are labeled according to (Zouni et al., 2001). No consistent changes were observed in helices D and E connecting donor and acceptor site or at the acceptor site itself. We do not detect any major rearrangements that could explain observations linking the redox potential of the primary quinone acceptor, QA, to Ca and/or Mn depletion of the PSII donor side (Krieger and Rutherford, 1997; Allakhverdiev et al., 2011; Brinkert et al., 2016). But this does not preclude more subtle structural changes from asserting such effect. We note that the side chain of Lys264 is insufficiently resolved in order to determine the distance from its Nζ to the carbonate species. The same ambiguity existed in earlier structures and it was unclear if Lys264 was a determinant of the protonation state of bicarbonate at the none-heme iron (discussed in [Brinkert et al., 2016]).
Figure 3—figure supplement 2. Increase in B-factors (blue, less flexible to red, more flexible) between PsbU and the WOC site in the unlocked (left) monomer, but much less so in the monomer locked by a crystal contact (right).
(A) Side chains binding the WOC in intact PSII, TyrZ and His190. (B) Slice through PSII as oriented in (D). Thick ribbons show the C-terminal loop of D1 and PsbU. (C) PSII viewed from the lumenal side compared to untreated PSII (E). (D) Contacts from symmetry related PSII molecules (grey) in the crystal.