6JLO image
Deposition Date 2019-03-06
Release Date 2019-10-16
Last Version Date 2024-10-23
Entry Detail
PDB ID:
6JLO
Keywords:
Title:
XFEL structure of cyanobacterial photosystem II (2F state, dataset2)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.20
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1
Gene (Uniprot):psbA
Chain IDs:A, U (auth: a)
Chain Length:344
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B, V (auth: b)
Chain Length:505
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C, W (auth: c)
Chain Length:455
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD
Chain IDs:D, X (auth: d)
Chain Length:342
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
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 vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, Z (auth: f)
Chain Length:44
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:G (auth: H), AA (auth: h)
Chain Length:65
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
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 vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J), CA (auth: j)
Chain Length:39
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:J (auth: K), DA (auth: k)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
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 vulcanus
Structures with similar UniProt ID
Protein Blast
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 vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O), GA (auth: o)
Chain Length:244
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein Y
Gene (Uniprot):psbY
Chain IDs:T (auth: R)
Chain Length:34
Number of Molecules:1
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:N (auth: T), HA (auth: t)
Chain Length:32
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:O (auth: U), IA (auth: u)
Chain Length:104
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:P (auth: V), JA (auth: v)
Chain Length:137
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein X
Gene (Uniprot):psbX
Chain IDs:R (auth: X), LA (auth: x)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Gene (Uniprot):psb30
Chain IDs:Q (auth: Y), KA (auth: y)
Chain Length:30
Number of Molecules:2
Biological Source:Thermosynechococcus vulcanus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
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 modified residue
Primary Citation
An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser.
Science 366 334 338 (2019)
PMID: 31624207 DOI: 10.1126/science.aax6998

Abstact

Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S0 to S4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S2, but flipping of D1 Glu189 upon transition to S3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

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Primary Citation of related structures
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