9M5A

cryo-EM structure of PSII D1-V185T from Thermosynechococcus vestitus BP-1

Summary for 9M5A

• Entry DOI: 10.2210/pdb9m5a/pdb
• Related: 7yq7
• EMDB information: 63639
• Descriptor: Photosystem II protein D1 3, Photosystem II reaction center protein L, Photosystem II reaction center protein M, ... (39 entities in total)
• Functional Keywords: psii mutation, photosynthesis
• Biological source: Thermosynechococcus vestitus BP-1; More
• Total number of polymer chains: 38
• Total formula weight: 744190.84

Authors

Jiang, H.W.,Nakajima, Y.,Akita, F.,Li, H.J.,Kato, K.,Sugiura, M.,Shen, J.R. (deposition date: 2025-03-05, release date: 2026-07-01, Last modification date: 2026-07-08)

Primary citation

Jiang, H.,Nakajima, Y.,Akita, F.,Li, H.,Kato, K.,Sugiura, M.,Shen, J.R.
Cryo-EM structure of photosystem II D1-V185T mutant from Thermosynechococcus vestitus.
Biochim Biophys Acta Bioenerg, 1867:149598-149598, 2026

PubMed Abstract: Photosystem II (PSII) catalyzes water oxidation into electrons, protons and dioxygen at its catalytic center, a MnCaO cluster, utilizing light energy. An amino acid residue D1-V185 in the D1 protein is located close to the MnCaO cluster, and plays a critical role in its catalytic function. In this research we purified PSII dimers from a D1-V185T mutant of Thermosynechococcus vestitus and analyzed its structure using low-damage cryo-electron microscopy (cryo-EM) at a resolution of 1.88 Å. The results revealed the presence of multi-conformations at the mutation site. Unlike the wild-type valine, which does not allow water molecules to be able to form hydrogen-bonds with it, both conformations of the mutant formed hydrogen bonds with nearby water molecules, which leads to rearrangement of the hydrogen bond networks in the O1 and Cl-1 channels. In conformation-A, the mutated Thr residue forms a hydrogen bond with a water molecule W6, which creates a new channel that bypasses the original O1 channel. Due to the hydrophilic OH group of Thr, the side-chain of D1-Glu189 was attracted and shifted toward the mutant Thr residue. In conformation-B, it forms a hydrogen bond with a water molecule W9 in the Cl-1 channel, bringing W9 closer and thereby disrupting the hydrogen bond network of the Cl-1 channel. In addition, multi-conformations of D2-K317, which is a ligand of Cl-1, were found in the mutant. These changes alter the environment surrounding the Cl-1 ion and MnCaO, thereby affecting the PSII water-oxidation activity.

PubMed: 42331212
DOI: 10.1016/j.bbabio.2026.149598

Experimental method

ELECTRON MICROSCOPY (1.88 Å)