7RF4 image
Deposition Date 2021-07-13
Release Date 2021-11-10
Last Version Date 2024-11-13
Entry Detail
PDB ID:
7RF4
Keywords:
Title:
RT XFEL structure of Photosystem II 50 microseconds after the second illumination at 2.27 Angstrom resolution
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.27 Å
R-Value Free:
0.24
R-Value Work:
0.18
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 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:510
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:461
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:352
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:84
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:45
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:66
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:38
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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 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:46
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:36
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain 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 elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein Y
Gene (Uniprot):psbY
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)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
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)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
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)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
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)
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 elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Gene (Uniprot):psb30
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)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:T (auth: Z), NA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
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