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TitleHigh-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.
Journal, issue, pagesCommun Biol, Vol. 4, Issue 1, Page 382, Year 2021
Publish dateMar 22, 2021
AuthorsKoji Kato / Naoyuki Miyazaki / Tasuku Hamaguchi / Yoshiki Nakajima / Fusamichi Akita / Koji Yonekura / Jian-Ren Shen /
PubMed AbstractPhotosystem 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 ...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.
External linksCommun Biol / PubMed:33753866 / PubMed Central
MethodsEM (single particle)
Resolution1.95 - 2.22 Å
Structure data

30547

7d1t

EMDB-30547, PDB-7d1t:
Cryo-EM Structure of PSII at 1.95 angstrom resolution
Method: EM (single particle) / Resolution: 1.95 Å

30548

7d1u

EMDB-30548, PDB-7d1u:
Cryo-EM Structure of PSII at 2.08 angstrom resolution
Method: EM (single particle) / Resolution: 2.08 Å

EMDB-30549:
Cryo-EM Structure of PSII at 2.22 angstrom resolution
Method: EM (single particle) / Resolution: 2.22 Å

EMDB-30550:
Cryo-EM Structure of PSII at 2.20 angstrom resolution
Method: EM (single particle) / Resolution: 2.2 Å

Chemicals

ChemComp-OEX:
CA-MN4-O5 CLUSTER

ChemComp-FE2:
Unknown entry

ChemComp-CL:
Unknown entry

ChemComp-CLA:
CHLOROPHYLL A

ChemComp-PHO:
PHEOPHYTIN A

ChemComp-BCR:
BETA-CAROTENE

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

ChemComp-PL9:
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE


ChemComp, No image

ChemComp-UNL:
Unknown ligand

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-MG:
Unknown entry

ChemComp-HEC:
HEME C

ChemComp-RRX:
(3R)-beta,beta-caroten-3-ol

ChemComp-HOH:
WATER

Source
  • thermosynechococcus vulcanus (bacteria)
KeywordsPHOTOSYNTHESIS / Photosystem II

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