Structure of C2S2M2-type PSII-FCPII supercomplex from diatom
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7vd5
Q-score: 0.543
Nagao R, Kato K, Kumazawa M, Ifuku K, Yokono M, Suzuki T, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR
Nat Commun (2022) 13 pp. 1764- [ DOI: doi:10.1038/s41467-022-29294-5 ]
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (24 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (16 kDa, Protein from Chaetoceros gracilis)
- Unknown ligand (Ligand)
- Photosystem ii subunit (4 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii d2 protein (37 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Extrinsic protein in photosystem ii (16 kDa, Protein from Chaetoceros gracilis)
- Bicarbonate ion (61 Da, Ligand)
- Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Chaetoceros gracilis)
- Fe (ii) ion (55 Da, Ligand)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Cytochrome b559 subunit beta (3 kDa, Protein from Chaetoceros gracilis)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Photosystem ii protein d1 (37 kDa, Protein from Chaetoceros gracilis)
- Pheophytin a (871 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
- C2s2m2-type psii-fcpii supercomplex (1 MDa, Complex from Chaetoceros gracilis)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chaetoceros gracilis)
- Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem ii reaction center protein w (5 kDa, Protein from Chaetoceros gracilis)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (17 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
- Ca-mn4-o5 cluster (339 Da, Ligand)
Structure of S1M1-type FCPII complex from diatom
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7vd6
Q-score: 0.565
Nagao R, Kato K, Kumazawa M, Ifuku K, Yokono M, Suzuki T, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR
Nat Commun (2022) 13 pp. 1764- [ DOI: doi:10.1038/s41467-022-29294-5 ]
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (29 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- S1m1-type fcpii complex (240 kDa, Complex from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (23 kDa, Protein from Chaetoceros gracilis)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (21 kDa, Protein from Chaetoceros gracilis)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Unknown ligand (Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- (3s,3's,5r,5'r,6s,6'r,8'r)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate (658 Da, Ligand)
- Water (18 Da, Ligand)
Structure of PSI tetramer from Anabaena
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6jeo
Q-score: 0.516
Kato K, Nagao R, Jiang TY, Ueno Y, Yokono M, Chan SK, Watanabe M, Ikeuchi M, Shen JR, Akimoto S, Miyazaki N, Akita F
Nat Commun (2019) 10 pp. 4929-4929 [ Pubmed: 31666526 DOI: doi:10.1038/s41467-019-12942-8 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit viii (5 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Photosystem i 4.8 kda protein (4 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Psi tetramer (1 MDa, Complex from Nostoc sp. PCC 7120)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Photosystem i reaction center subunit iii (17 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Photosystem i reaction center subunit xi (18 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit xii (4 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit ix (5 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Photosystem i p700 chlorophyll a apoprotein a2 1 (83 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit psak 1 (8 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Structure of PSI dimer from Anabaena
Kato K, Nagao R, Jiang TY, Ueno Y, Yokono M, Chan SK, Watanabe M, Ikeuchi M, Shen JR, Akimoto S, Miyazaki N, Akita F
Nat Commun (2019) 10 pp. 4929-4929 [ Pubmed: 31666526 DOI: doi:10.1038/s41467-019-12942-8 ]
- Psi dimer (700 kDa, Complex from Nostoc sp. PCC 7120)