5MX2 image
Deposition Date 2017-01-20
Release Date 2017-08-02
Last Version Date 2024-10-09
Entry Detail
PDB ID:
5MX2
Keywords:
Title:
Photosystem II depleted of the Mn4CaO5 cluster at 2.55 A resolution
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.25
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1 1
Gene (Uniprot):psbA1
Chain IDs:A, T (auth: a)
Chain Length:344
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B, U (auth: b)
Chain Length:510
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C, V (auth: c)
Chain Length:461
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD1, psbD2
Chain IDs:D, W (auth: d)
Chain Length:352
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, X (auth: e)
Chain Length:84
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, Y (auth: f)
Chain Length:45
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:G (auth: H), Z (auth: h)
Chain Length:66
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:H (auth: I), AA (auth: i)
Chain Length:38
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J), BA (auth: j)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:J (auth: K), CA (auth: k)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:K (auth: L), DA (auth: l)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:L (auth: M), EA (auth: m)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O), FA (auth: o)
Chain Length:272
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein Y
Gene (Uniprot):psbY
Chain IDs:KA (auth: R), LA (auth: r)
Chain Length:41
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:N (auth: T), GA (auth: t)
Chain Length:32
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:O (auth: U), HA (auth: u)
Chain Length:134
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:P (auth: V), IA (auth: v)
Chain Length:163
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center X protein
Gene (Uniprot):psbX
Chain IDs:R (auth: X), JA (auth: x)
Chain Length:41
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Gene (Uniprot):psb30
Chain IDs:Q (auth: Y), MA (auth: y)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:S (auth: Z), NA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Thermosynechococcus vestitus BP-1
Primary Citation
Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II.
Elife 6 ? ? (2017)
PMID: 28718766 DOI: 10.7554/eLife.26933

Abstact

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn4CaO5-cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn4CaO5-cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn4CaO5-cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn4CaO5-cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.

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Primary Citation of related structures