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High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.

<div class='caption-title'>B-factor plot for the datasets of Titan-75k, Titan-96k, and ARM-60k.</div>
<div class='caption-title'>Overall structure of PSII at a high-dose.</div>
<div class='caption-title'>Electron beam damages in the PSII structure of the ARM-60k dataset at the high-dose (83 e−Å−2) and low-dose (3.3 e−Å−2).</div>
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR
OpenAccess logo Commun Biol 4 382 (2021)
Cited: 27 times
EuropePMC logo PMID: 33753866

Abstract

Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

Reviews - 7d1u mentioned but not cited (1)

  1. New Structural and Mechanistic Insights Into Functional Roles of Cytochrome b 559 in Photosystem II. Chiu YF, Chu HA. Front Plant Sci 13 914922 (2022)

Articles - 7d1u mentioned but not cited (2)

  1. High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams. Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR. Commun Biol 4 382 (2021)
  2. Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning. Amin M. Photosynth Res 156 89-100 (2023)


Reviews citing this publication (6)

  1. Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function. Hussein R, Ibrahim M, Bhowmick A, Simon PS, Bogacz I, Doyle MD, Dobbek H, Zouni A, Messinger J, Yachandra VK, Kern JF, Yano J. Photosynth Res 158 91-107 (2023)
  2. Analysis and comparison of electron radiation damage assessments in Cryo-EM by single particle analysis and micro-crystal electron diffraction. Shi D, Huang R. Front Mol Biosci 9 988928 (2022)
  3. Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination. Xue H, Zhang M, Liu J, Wang J, Ren G. Front Chem 10 889203 (2022)
  4. Mimicking the Oxygen-Evolving Center in Photosynthesis. Chen Y, Xu B, Yao R, Chen C, Zhang C. Front Plant Sci 13 929532 (2022)
  5. Processing of D1 Protein: A Mysterious Process Carried Out in Thylakoid Lumen. Inagaki N. Int J Mol Sci 23 2520 (2022)
  6. Solar energy conversion by photosystem II: principles and structures. Shevela D, Kern JF, Govindjee G, Messinger J. Photosynth Res (2023)

Articles citing this publication (18)

  1. Assembly of D1/D2 complexes of photosystem II: Binding of pigments and a network of auxiliary proteins. Knoppová J, Sobotka R, Yu J, Bečková M, Pilný J, Trinugroho JP, Csefalvay L, Bína D, Nixon PJ, Komenda J. Plant Physiol 189 790-804 (2022)
  2. High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803. Gisriel CJ, Wang J, Liu J, Flesher DA, Reiss KM, Huang HL, Yang KR, Armstrong WH, Gunner MR, Batista VS, Debus RJ, Brudvig GW. Proc Natl Acad Sci U S A 119 e2116765118 (2022)
  3. Glycerol binding at the narrow channel of photosystem II stabilizes the low-spin S2 state of the oxygen-evolving complex. Flesher DA, Liu J, Wiwczar JM, Reiss K, Yang KR, Wang J, Askerka M, Gisriel CJ, Batista VS, Brudvig GW. Photosynth Res 152 167-175 (2022)
  4. How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM. Wang J, Liu J, Gisriel CJ, Wu S, Maschietto F, Flesher DA, Lolis E, Lisi GP, Brudvig GW, Xiong Y, Batista VS. J Struct Biol 214 107902 (2022)
  5. LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins. Ansell TB, Song W, Coupland CE, Carrique L, Corey RA, Duncan AL, Cassidy CK, Geurts MMG, Rasmussen T, Ward AB, Siebold C, Stansfeld PJ, Sansom MSP. Nat Commun 14 7774 (2023)
  6. Structure of Dunaliella photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes. Caspy I, Fadeeva M, Mazor Y, Nelson N. Elife 12 e81150 (2023)
  7. The structure of natively iodinated bovine thyroglobulin. Kim K, Kopylov M, Bobe D, Kelley K, Eng ET, Arvan P, Clarke OB. Acta Crystallogr D Struct Biol 77 1451-1459 (2021)
  8. An LH1-RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteins. Tani K, Kanno R, Kurosawa K, Takaichi S, Nagashima KVP, Hall M, Yu LJ, Kimura Y, Madigan MT, Mizoguchi A, Humbel BM, Wang-Otomo ZY. Commun Biol 5 1197 (2022)
  9. Comparison of PsbQ and Psb27 in photosystem II provides insight into their roles. Gisriel CJ, Brudvig GW. Photosynth Res (2022)
  10. DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images. Hamitouche I, Jonic S. Front Mol Biosci 9 965645 (2022)
  11. Functional Water Networks in Fully Hydrated Photosystem II. Sirohiwal A, Pantazis DA. J Am Chem Soc 144 22035-22050 (2022)
  12. It started with a Cys: Spontaneous cysteine modification during cryo-EM grid preparation. Klebl DP, Wang Y, Sobott F, Thompson RF, Muench SP. Front Mol Biosci 9 945772 (2022)
  13. MDSPACE and MDTOMO Software for Extracting Continuous Conformational Landscapes from Datasets of Single Particle Images and Subtomograms Based on Molecular Dynamics Simulations: Latest Developments in ContinuousFlex Software Package. Vuillemot R, Harastani M, Hamitouche I, Jonic S. Int J Mol Sci 25 20 (2023)
  14. Mutation of a metal ligand stabilizes the high-spin form of the S2 state in the O2-producing Mn4CaO5 cluster of photosystem II. Chakarawet K, Debus RJ, Britt RD. Photosynth Res 156 309-314 (2023)
  15. editorial Radiation damage to biological samples: still a pertinent issue. Garman EF, Weik M. J Synchrotron Radiat 28 1278-1283 (2021)
  16. Structural insights into the action mechanisms of artificial electron acceptors in photosystem II. Kamada S, Nakajima Y, Shen JR. J Biol Chem 299 104839 (2023)
  17. Structural principles of B cell antigen receptor assembly. Dong Y, Pi X, Bartels-Burgahn F, Saltukoglu D, Liang Z, Yang J, Alt FW, Reth M, Wu H. Nature 612 156-161 (2022)
  18. Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography. Doyle MD, Bhowmick A, Wych DC, Lassalle L, Simon PS, Holton J, Sauter NK, Yachandra VK, Kern JF, Yano J, Wall ME. J Am Chem Soc 145 14621-14635 (2023)


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