7EDA image
Deposition Date 2021-03-15
Release Date 2021-07-07
Last Version Date 2025-06-25
Entry Detail
PDB ID:
7EDA
Keywords:
Title:
Structure of monomeric photosystem II
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.78 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1
Gene (Uniprot):psbA
Chain IDs:A
Chain Length:334
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B
Chain Length:504
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C
Chain Length:451
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD
Chain IDs:D
Chain Length:341
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E
Chain Length:84
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F
Chain Length:45
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:G (auth: H)
Chain Length:62
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:H (auth: I)
Chain Length:38
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J)
Chain Length:40
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:J (auth: K)
Chain Length:37
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:K (auth: L)
Chain Length:37
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:L (auth: M)
Chain Length:30
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O)
Chain Length:244
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein Y
Gene (Uniprot):psbY
Chain IDs:T (auth: R)
Chain Length:34
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:N (auth: T)
Chain Length:30
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:O (auth: U)
Chain Length:104
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:P (auth: V)
Chain Length:163
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein X
Gene (Uniprot):psbX
Chain IDs:R (auth: X)
Chain Length:40
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Gene (Uniprot):psb30
Chain IDs:Q (auth: Y)
Chain Length:30
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:S (auth: Z)
Chain Length:62
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME H MET modified residue
HSK D HIS modified residue
Primary Citation
Cryo-EM structure of monomeric photosystem II at 2.78 angstrom resolution reveals factors important for the formation of dimer.
Biochim Biophys Acta Bioenerg 1862 148471 148471 (2021)
PMID: 34216574 DOI: 10.1016/j.bbabio.2021.148471

Abstact

Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.

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Primary Citation of related structures