8F4C image
Deposition Date 2022-11-10
Release Date 2023-03-22
Last Version Date 2024-11-06
Entry Detail
PDB ID:
8F4C
Keywords:
Title:
RT XFEL structure of the two-flash state of Photosystem II (2F, S3-rich) at 2.00 Angstrom resolution
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.22
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1 1
Gene (Uniprot):psbA1
Chain IDs:A, U (auth: a)
Chain Length:344
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B, V (auth: b)
Chain Length:510
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C, W (auth: c)
Chain Length:461
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD1, psbD2
Chain IDs:D, X (auth: d)
Chain Length:352
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, Y (auth: e)
Chain Length:84
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, Z (auth: f)
Chain Length:45
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:G (auth: H), AA (auth: h)
Chain Length:66
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:H (auth: I), BA (auth: i)
Chain Length:38
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J), CA (auth: j)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:J (auth: K), DA (auth: k)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:K (auth: L), EA (auth: l)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:L (auth: M), FA (auth: m)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O), GA (auth: o)
Chain Length:272
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein Y
Gene (Uniprot):psbY
Chain IDs:T (auth: R), NA (auth: r)
Chain Length:41
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:N (auth: T), HA (auth: t)
Chain Length:32
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:O (auth: U), IA (auth: u)
Chain Length:134
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:P (auth: V), JA (auth: v)
Chain Length:163
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center X protein
Gene (Uniprot):psbX
Chain IDs:R (auth: X), LA (auth: x)
Chain Length:41
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Gene (Uniprot):psb30
Chain IDs:Q (auth: Y), KA (auth: y)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:S (auth: Z), MA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME L MET modified residue
Primary Citation

Abstact

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

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Primary Citation of related structures