8IWH image
Deposition Date 2023-03-30
Release Date 2023-10-25
Last Version Date 2024-11-13
Entry Detail
PDB ID:
8IWH
Keywords:
Title:
Structure and characteristics of a photosystem II supercomplex containing monomeric LHCX and dimeric FCPII antennae from the diatom Thalassiosira pseudonana
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.68 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Fucoxanthin chl a/c protein, lhca clade
Gene (Uniprot):Lhca2
Chain IDs:OA (auth: 3)
Chain Length:220
Number of Molecules:1
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Fucoxanthin-chlorophyll a-c binding protein, plastid
Gene (Uniprot):Lhcf11
Chain IDs:PA (auth: 4)
Chain Length:196
Number of Molecules:1
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Fucoxanthin chlorophyll a/c protein 6
Gene (Uniprot):Lhcf6
Chain IDs:QA (auth: 5)
Chain Length:192
Number of Molecules:1
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Fucoxanthin chlorophyll a/c protein 5
Gene (Uniprot):Lhcf5
Chain IDs:RA (auth: 6)
Chain Length:199
Number of Molecules:1
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Fucoxanthin chlorophyll a/c protein-LI818 clade
Gene (Uniprot):Lhcx6_1
Chain IDs:SA (auth: 7), ZA (auth: 0)
Chain Length:199
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Fucoxanthin chlorophyll a/c light-harvesting protein, major type
Gene (Uniprot):Lhcf7
Chain IDs:AB (auth: 9), BB (auth: 2), CB (auth: 8), DB (auth: 1)
Chain Length:193
Number of Molecules:4
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1
Gene (Uniprot):psbA
Chain IDs:A, TA (auth: a)
Chain Length:333
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B, UA (auth: b)
Chain Length:509
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C, D (auth: c)
Chain Length:470
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD
Chain IDs:E (auth: D), F (auth: d)
Chain Length:351
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:G (auth: E), H (auth: e)
Chain Length:84
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:I (auth: F), J (auth: f)
Chain Length:43
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II Psb31 protein domain-containing protein
Gene (Uniprot):THAPSDRAFT_24769
Chain IDs:K (auth: G), L (auth: g)
Chain Length:176
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:M (auth: H), N (auth: h)
Chain Length:66
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:O (auth: I), P (auth: i)
Chain Length:34
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:Q (auth: J), R (auth: j)
Chain Length:39
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:S (auth: K), T (auth: k)
Chain Length:44
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:U (auth: L), V (auth: l)
Chain Length:38
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center M protein, plastid
Gene (Uniprot):PsbM
Chain IDs:W (auth: M), X (auth: m)
Chain Length:113
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Oxygen-evolving enhancer protein 1
Gene (Uniprot):PsbO
Chain IDs:AA (auth: O), BA (auth: o)
Chain Length:305
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II subunit, PsbQ.
Gene (Uniprot):THAPSDRAFT_20603
Chain IDs:XA (auth: Q), YA (auth: q)
Chain Length:211
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:CA (auth: T), DA (auth: t)
Chain Length:28
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:PS II complex 12 kDa extrinsic protein
Gene (Uniprot):THAPSDRAFT_2848
Chain IDs:EA (auth: U), FA (auth: u)
Chain Length:148
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:GA (auth: V), HA (auth: v)
Chain Length:162
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II subunit, PsbW
Gene (Uniprot):THAPSDRAFT_24099
Chain IDs:IA (auth: W), JA (auth: w)
Chain Length:54
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center X protein
Gene (Uniprot):psbX
Chain IDs:KA (auth: X), LA (auth: x)
Chain Length:38
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Gene (Uniprot):psb30
Chain IDs:VA (auth: Y), WA (auth: y)
Chain Length:34
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:MA (auth: Z), NA (auth: z)
Chain Length:61
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Polymer Type:polypeptide(L)
Molecule:Photosystem II subunit, PsbN.
Chain IDs:Y (auth: n), Z (auth: N)
Chain Length:30
Number of Molecules:2
Biological Source:Thalassiosira pseudonana
Primary Citation
Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII.
Sci Adv 9 eadi8446 eadi8446 (2023)
PMID: 37878698 DOI: 10.1126/sciadv.adi8446

Abstact

Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from Thalassiosira pseudonana at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls a/c is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms.

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