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Structure paper

TitleThe Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 4681, Year 2023
Publish dateAug 4, 2023
AuthorsZiyu Zhao / Irene Vercellino / Jana Knoppová / Roman Sobotka / James W Murray / Peter J Nixon / Leonid A Sazanov / Josef Komenda /
PubMed AbstractRobust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly ...Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising MnCaO cluster, thereby preventing the premature binding of Mn and Ca ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the MnCaO cluster.
External linksNat Commun / PubMed:37542031 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.15 Å
Structure data

15522

8am5

EMDB-15522, PDB-8am5:
RCII/PSI complex, class 3
Method: EM (single particle) / Resolution: 3.1 Å

15618

8asl

EMDB-15618, PDB-8asl:
RCII/PSI complex, class 2
Method: EM (single particle) / Resolution: 3.15 Å

15621

8asp

EMDB-15621, PDB-8asp:
RCII/PSI complex, focused refinement of PSI
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-FE2:
Unknown entry

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

ChemComp-PHO:
PHEOPHYTIN A / Pheophytin

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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

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

ChemComp-45D:
beta,beta-carotene-4,4'-dione / Canthaxanthin

ChemComp-ECH:
beta,beta-caroten-4-one / Echinenone

ChemComp-EQ3:
(3'R)-3'-hydroxy-beta,beta-caroten-4-one / 3'-Hydroxyechinenone

ChemComp-ZEX:
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol

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

Source
  • synechocystis sp. pcc 6803 (bacteria)
KeywordsPHOTOSYNTHESIS / photosystem / assembly factor / membrane protein

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