7RF8 image
Entry Detail
PDB ID:
7RF8
Keywords:
Title:
RT XFEL structure of the two-flash state of Photosystem II (2F, S3-rich) at 2.09 Angstrom resolution
Biological Source:
PDB Version:
Deposition Date:
2021-07-13
Release Date:
2021-11-10
Method Details:
Experimental Method:
Resolution:
2.09 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Photosystem II protein D1 1
Chain IDs:A, U (auth: a)
Chain Length:344
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II CP47 reaction center protein
Chain IDs:B, V (auth: b)
Chain Length:510
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II CP43 reaction center protein
Chain IDs:C, W (auth: c)
Chain Length:461
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II D2 protein
Chain IDs:D, X (auth: d)
Chain Length:352
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit alpha
Chain IDs:E, Y (auth: e)
Chain Length:84
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit beta
Chain IDs:F, Z (auth: f)
Chain Length:45
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein H
Chain IDs:G (auth: H), AA (auth: h)
Chain Length:66
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein I
Chain IDs:H (auth: I), BA (auth: i)
Chain Length:38
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein J
Chain IDs:I (auth: J), CA (auth: j)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein K
Chain IDs:J (auth: K), DA (auth: k)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein L
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)
Description:Photosystem II reaction center protein M
Chain IDs:L (auth: M), FA (auth: m)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II manganese-stabilizing polypeptide
Chain IDs:M (auth: O), GA (auth: o)
Chain Length:272
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II protein Y
Chain IDs:N (auth: R), HA (auth: r)
Chain Length:41
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein T
Chain IDs:O (auth: T), IA (auth: t)
Chain Length:32
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II 12 kDa extrinsic protein
Chain IDs:P (auth: U), JA (auth: u)
Chain Length:134
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Cytochrome c-550
Chain IDs:Q (auth: V), KA (auth: v)
Chain Length:163
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center X protein
Chain IDs:R (auth: X), LA (auth: x)
Chain Length:41
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Ycf12
Chain IDs:S (auth: Y), MA (auth: y)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Z
Chain IDs:T (auth: Z), NA (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

Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.

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Primary Citation of related structures