6DHH image
Deposition Date 2018-05-20
Release Date 2018-11-21
Last Version Date 2024-11-06
Entry Detail
PDB ID:
6DHH
Keywords:
Title:
RT XFEL structure of Photosystem II 400 microseconds after the second illumination at 2.2 Angstrom resolution
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.26
R-Value Work:
0.19
R-Value Observed:
0.19
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:334
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B, V (auth: b)
Chain Length:505
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C, W (auth: c)
Chain Length:451
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD1, psbD2
Chain IDs:D, X (auth: d)
Chain Length:341
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, Y (auth: e)
Chain Length:82
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, Z (auth: f)
Chain Length:34
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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:65
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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:36
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J), CA (auth: j)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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:37
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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 elongatus (strain 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:33
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O), GA (auth: o)
Chain Length:244
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein Y
Gene (Uniprot):psbY
Chain IDs:T (auth: R), NA (auth: r)
Chain Length:34
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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:30
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:O (auth: U), IA (auth: u)
Chain Length:97
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:P (auth: V), JA (auth: v)
Chain Length:137
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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:38
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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:30
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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 elongatus (strain BP-1)
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME H MET modified residue
Primary Citation

Abstact

Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle1,2. The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex3-7. This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08 Å). In addition, we report structures of two transient states at 150 and 400 µs, revealing notable structural changes including the binding of one additional 'water', Ox, during the S2→S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.

Legend

Protein

Chemical

Disease

Primary Citation of related structures