4IL6 image
Entry Detail
PDB ID:
4IL6
Title:
Structure of Sr-substituted photosystem II
Biological Source:
PDB Version:
Deposition Date:
2012-12-29
Release Date:
2013-03-06
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Photosystem Q(B) protein
Chain IDs:A, U (auth: a)
Chain Length:334
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II core light harvesting protein
Chain IDs:B, V (auth: b)
Chain Length:505
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II CP43 protein
Chain IDs:C, W (auth: c)
Chain Length:451
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II D2 protein
Chain IDs:D, X (auth: d)
Chain Length:342
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit alpha
Chain IDs:E, Y (auth: e)
Chain Length:80
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit beta
Chain IDs:F, Z (auth: f)
Chain Length:34
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein H
Chain IDs:G (auth: H), AA (auth: h)
Chain Length:63
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein I
Chain IDs:H (auth: I), BA (auth: i)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein J
Chain IDs:I (auth: J), CA (auth: j)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein K
Chain IDs:J (auth: K), DA (auth: k)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
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 vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein M
Chain IDs:L (auth: M), FA (auth: m)
Chain Length:34
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II manganese-stabilizing polypeptide
Chain IDs:M (auth: O), GA (auth: o)
Chain Length:244
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II protein Y
Chain IDs:T (auth: R)
Chain Length:34
Number of Molecules:1
Biological Source:Thermosynechococcus elongatus BP-1
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein T
Chain IDs:N (auth: T), HA (auth: t)
Chain Length:31
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II 12 kDa extrinsic protein
Chain IDs:O (auth: U), IA (auth: u)
Chain Length:97
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Cytochrome c-550
Chain IDs:P (auth: V), JA (auth: v)
Chain Length:137
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein X
Chain IDs:R (auth: X), LA (auth: x)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein ycf12
Chain IDs:Q (auth: Y), KA (auth: y)
Chain Length:30
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Z
Chain IDs:S (auth: Z), MA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME H MET N-FORMYLMETHIONINE
Primary Citation
Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation
Proc.Natl.Acad.Sci.USA 110 3889 3894 (2013)
PMID: 23426624 DOI: 10.1073/pnas.1219922110

Abstact

Oxygen-evolving complex of photosystem II (PSII) is a tetra-manganese calcium penta-oxygenic cluster (Mn4CaO5) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca(2+) in this cluster and the possible location of water substrates in this process, we crystallized Sr(2+)-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2.1 Å, and compared it with the 1.9 Å structure of native PSII. Our analysis showed that the position of Sr was moved toward the outside of the cubane structure of the Mn4CaO5-cluster relative to that of Ca(2+), resulting in a general elongation of the bond distances between Sr and its surrounding atoms compared with the corresponding distances in the Ca-containing cluster. In particular, we identified an apparent elongation in the bond distance between Sr and one of the two terminal water ligands of Ca(2+), W3, whereas that of the Sr-W4 distance was not much changed. This result may contribute to the decrease of oxygen evolution upon Sr(2+)-substitution, and suggests a weak binding and rather mobile nature of this particular water molecule (W3), which in turn implies the possible involvement of this water molecule as a substrate in the O-O bond formation. In addition, the PsbY subunit, which was absent in the 1.9 Å structure of native PSII, was found in the Sr-PSII structure.

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