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RT XFEL structure of the one-flash state of Photosystem II (1F, S2-rich) at 2.08 Angstrom resolution

Source organism: Thermosynechococcus vestitus BP-1
Biochemical function: metal ion binding
Biological process: photosynthesis
Cellular component: photosystem II

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EC 1.10.3.9: Photosystem II

Reaction catalysed:
2 H(2)O + 2 plastoquinone + 4 light = O(2) + 2 plastoquinol
Systematic name:
H(2)O:plastoquinone reductase (light-dependent)

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00283
Domain description: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits
Occurring in:
  1. Cytochrome b559 subunit alpha
  2. Cytochrome b559 subunit beta
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF00283 (Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits) in Cytochrome b559 subunit alpha. Showing 1 copy in chain Y [auth e].
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF00283 (Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits) in Cytochrome b559 subunit beta. Showing 1 copy in chain F.

PF00421
Domain description: Photosystem II protein
Occurring in:
  1. Photosystem II CP47 reaction center protein
  2. Photosystem II CP43 reaction center protein
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF00421 (Photosystem II protein) in Photosystem II CP47 reaction center protein. Showing 1 copy in chain B.
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF00421 (Photosystem II protein) in Photosystem II CP43 reaction center protein. Showing 1 copy in chain W [auth c].

PF00124
Domain description: Photosynthetic reaction centre protein
Occurring in:
  1. Photosystem II protein D1 1
  2. Photosystem II D2 protein
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF00124 (Photosynthetic reaction centre protein) in Photosystem II protein D1 1. Showing 1 copy in chain A.
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF00124 (Photosynthetic reaction centre protein) in Photosystem II D2 protein. Showing 1 copy in chain D.

PF01737
Domain description: YCF9
Occurring in:
  1. Photosystem II reaction center protein Z
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF01737 (YCF9) in Photosystem II reaction center protein Z. Showing 1 copy in chain S [auth Z].

PF05969
Domain description: Photosystem II complex subunit Ycf12
Occurring in:
  1. Photosystem II reaction center protein Psb30
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF05969 (Photosystem II complex subunit Ycf12) in Photosystem II reaction center protein Psb30. Showing 1 copy in chain KA [auth y].

PF06596
Domain description: Photosystem II reaction centre X protein (PsbX)
Occurring in:
  1. Photosystem II reaction center protein X
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF06596 (Photosystem II reaction centre X protein (PsbX)) in Photosystem II reaction center protein X. Showing 1 copy in chain R [auth X].

PF14495
Domain description: Cytochrome c-550 domain
Occurring in:
  1. Photosystem II extrinsic protein V
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF14495 (Cytochrome c-550 domain) in Photosystem II extrinsic protein V. Showing 1 copy in chain P [auth V].

PF06514
Domain description: Photosystem II 12 kDa extrinsic protein (PsbU)
Occurring in:
  1. Photosystem II extrinsic protein U
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF06514 (Photosystem II 12 kDa extrinsic protein (PsbU)) in Photosystem II extrinsic protein U. Showing 1 copy in chain O [auth U].

PF01405
Domain description: Photosystem II reaction centre T protein
Occurring in:
  1. Photosystem II reaction center protein T
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF01405 (Photosystem II reaction centre T protein) in Photosystem II reaction center protein T. Showing 1 copy in chain N [auth T].

PF06298
Domain description: Photosystem II protein Y (PsbY)
Occurring in:
  1. Photosystem II reaction center protein Y
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF06298 (Photosystem II protein Y (PsbY)) in Photosystem II reaction center protein Y. Showing 1 copy in chain T [auth R].

PF01716
Domain description: Manganese-stabilising protein / photosystem II polypeptide
Occurring in:
  1. Photosystem II extrinsic protein O
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF01716 (Manganese-stabilising protein / photosystem II polypeptide) in Photosystem II extrinsic protein O. Showing 1 copy in chain M [auth O].

PF05151
Domain description: Photosystem II reaction centre M protein (PsbM)
Occurring in:
  1. Photosystem II reaction center protein M
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF05151 (Photosystem II reaction centre M protein (PsbM)) in Photosystem II reaction center protein M. Showing 1 copy in chain L [auth M].

PF02419
Domain description: PsbL protein
Occurring in:
  1. Photosystem II reaction center protein L
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF02419 (PsbL protein) in Photosystem II reaction center protein L. Showing 1 copy in chain K [auth L].

PF02533
Domain description: Photosystem II 4 kDa reaction centre component
Occurring in:
  1. Photosystem II reaction center protein K
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF02533 (Photosystem II 4 kDa reaction centre component) in Photosystem II reaction center protein K. Showing 1 copy in chain J [auth K].

PF01788
Domain description: PsbJ
Occurring in:
  1. Photosystem II reaction center protein J
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF01788 (PsbJ) in Photosystem II reaction center protein J. Showing 1 copy in chain I [auth J].

PF02532
Domain description: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
Occurring in:
  1. Photosystem II reaction center protein I
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF02532 (Photosystem II reaction centre I protein (PSII 4.8 kDa protein)) in Photosystem II reaction center protein I. Showing 1 copy in chain H [auth I].

PF00737
Domain description: Photosystem II 10 kDa phosphoprotein
Occurring in:
  1. Photosystem II reaction center protein H
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF00737 (Photosystem II 10 kDa phosphoprotein) in Photosystem II reaction center protein H. Showing 1 copy in chain G [auth H].

PF00284
Domain description: Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit
Occurring in:
  1. Cytochrome b559 subunit alpha
The deposited structure of PDB entry 6dhf contains 2 copies of Pfam domain PF00284 (Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit) in Cytochrome b559 subunit alpha. Showing 1 copy in chain Y [auth e].

InterPro InterPro annotations
IPR000484
Domain description: Photosynthetic reaction centre, L/M
Occurring in:
  1. Photosystem II protein D1 1
  2. Photosystem II D2 protein
IPR036854
Domain description: Photosystem II protein D1/D2 superfamily
Occurring in:
  1. Photosystem II protein D1 1
  2. Photosystem II D2 protein
IPR002644
Domain description: Photosystem II PsbZ, reaction centre
Occurring in:
  1. Photosystem II reaction center protein Z
IPR007826
Domain description: Photosystem II PsbM
Occurring in:
  1. Photosystem II reaction center protein M
IPR001056
Domain description: Photosystem II reaction centre protein H
Occurring in:
  1. Photosystem II reaction center protein H
IPR006217
Domain description: Photosystem II cytochrome b559, alpha subunit
Occurring in:
  1. Cytochrome b559 subunit alpha
IPR036909
Domain description: Cytochrome c-like domain superfamily
Occurring in:
  1. Photosystem II extrinsic protein V
IPR017851
Domain description: Photosystem II extrinsic protein V, cytochrome c-550 precursor
Occurring in:
  1. Photosystem II extrinsic protein V
IPR002628
Domain description: Photosystem II extrinsic protein O
Occurring in:
  1. Photosystem II extrinsic protein O
IPR002682
Domain description: Photosystem II PsbJ
Occurring in:
  1. Photosystem II reaction center protein J
IPR036863
Domain description: Photosystem II reaction centre protein H superfamily
Occurring in:
  1. Photosystem II reaction center protein H
IPR006216
Domain description: Photosystem II cytochrome b559, conserved site
Occurring in:
  1. Cytochrome b559 subunit alpha
  2. Cytochrome b559 subunit beta
IPR013081
Domain description: Photosystem II cytochrome b559, N-terminal
Occurring in:
  1. Cytochrome b559 subunit alpha
  2. Cytochrome b559 subunit beta
IPR005868
Domain description: Photosystem II D2 protein
Occurring in:
  1. Photosystem II D2 protein
IPR005869
Domain description: Photosystem II CP43 reaction centre protein
Occurring in:
  1. Photosystem II CP43 reaction center protein
IPR036001
Domain description: Photosystem antenna protein-like superfamily
Occurring in:
  1. Photosystem II CP47 reaction center protein
  2. Photosystem II CP43 reaction center protein
IPR017486
Domain description: Photosystem II CP47 reaction centre protein
Occurring in:
  1. Photosystem II CP47 reaction center protein
IPR000932
Domain description: Photosystem antenna protein-like
Occurring in:
  1. Photosystem II CP47 reaction center protein
  2. Photosystem II CP43 reaction center protein
IPR036512
Domain description: Photosystem II PsbZ superfamily
Occurring in:
  1. Photosystem II reaction center protein Z
IPR010284
Domain description: Photosystem II reaction center protein Ycf12
Occurring in:
  1. Photosystem II reaction center protein Psb30
IPR023431
Domain description: Photosystem II PsbX, type 1 subfamily
Occurring in:
  1. Photosystem II reaction center protein X
IPR009518
Domain description: Photosystem II PsbX
Occurring in:
  1. Photosystem II reaction center protein X
IPR009056
Domain description: Cytochrome c-like domain
Occurring in:
  1. Photosystem II extrinsic protein V
IPR029490
Domain description: Cytochrome c-550 domain
Occurring in:
  1. Photosystem II extrinsic protein V
IPR016003
Domain description: Photosystem II extrinsic protein V, cytochrome c-550 precursor-like
Occurring in:
  1. Photosystem II extrinsic protein V
IPR010527
Domain description: Photosystem II PsbU, oxygen evolving complex
Occurring in:
  1. Photosystem II extrinsic protein U
IPR037268
Domain description: Photosystem II PsbT superfamily
Occurring in:
  1. Photosystem II reaction center protein T
IPR001743
Domain description: Photosystem II PsbT
Occurring in:
  1. Photosystem II reaction center protein T
IPR009388
Domain description: Photosystem II PsbY
Occurring in:
  1. Photosystem II reaction center protein Y
IPR011250
Domain description: Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Occurring in:
  1. Photosystem II extrinsic protein O
IPR037269
Domain description: Photosystem II PsbM superfamily
Occurring in:
  1. Photosystem II reaction center protein M
IPR037266
Domain description: Photosystem II PsbL superfamily
Occurring in:
  1. Photosystem II reaction center protein L
IPR003372
Domain description: Photosystem II PsbL
Occurring in:
  1. Photosystem II reaction center protein L
IPR037270
Domain description: Photosystem II PsbK superfamily
Occurring in:
  1. Photosystem II reaction center protein K
IPR003687
Domain description: Photosystem II PsbK
Occurring in:
  1. Photosystem II reaction center protein K
IPR037267
Domain description: Photosystem II PsbJ superfamily
Occurring in:
  1. Photosystem II reaction center protein J
IPR037271
Domain description: Photosystem II PsbI superfamily
Occurring in:
  1. Photosystem II reaction center protein I
IPR003686
Domain description: Photosystem II PsbI
Occurring in:
  1. Photosystem II reaction center protein I
IPR006241
Domain description: Photosystem II cytochrome b559, beta subunit
Occurring in:
  1. Cytochrome b559 subunit beta
IPR013082
Domain description: Photosystem II cytochrome b559, alpha subunit, lumenal region
Occurring in:
  1. Cytochrome b559 subunit alpha
IPR037025
Domain description: Photosystem II cytochrome b559, alpha subunit superfamily
Occurring in:
  1. Cytochrome b559 subunit alpha
IPR044900
Domain description: Photosystem II CP43 reaction centre protein superfamily
Occurring in:
  1. Photosystem II CP43 reaction center protein
IPR005867
Domain description: Photosystem II protein D1
Occurring in:
  1. Photosystem II protein D1 1

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