4UB6 image
Entry Detail
PDB ID:
4UB6
Title:
Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser
Biological Source:
PDB Version:
Deposition Date:
2014-08-12
Release Date:
2014-12-03
Method Details:
Experimental Method:
Resolution:
1.95 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
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:344
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II CP47 chlorophyll apoprotein
Chain IDs:B, V (auth: b)
Chain Length:505
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II 44 kDa reaction center protein
Chain IDs:C, W (auth: c)
Chain Length:455
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:84
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:44
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:65
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:38
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:39
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:36
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 vulcanus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein T
Chain IDs:N (auth: T), HA (auth: t)
Chain Length:32
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:104
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
Primary Citation
Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.
Nature 517 99 103 (2015)
PMID: 25470056 DOI: 10.1038/nature13991

Abstact

Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation, and slight differences were found in the Mn-Mn distances determined by XRD, EXAFS and theoretical studies. Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.

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