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 ]
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (24 kDa, Protein from Chaetoceros gracilis)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Chaetoceros gracilis)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
- Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii subunit (4 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (16 kDa, Protein from Chaetoceros gracilis)
- Cytochrome b559 subunit beta (3 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chaetoceros gracilis)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii d2 protein (37 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii protein d1 (37 kDa, Protein from Chaetoceros gracilis)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 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)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Pheophytin a (871 Da, Ligand)
- Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
- Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein 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)
- (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)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (16 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein w (5 kDa, Protein from Chaetoceros gracilis)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- C2s2m2-type psii-fcpii supercomplex (1 MDa, Complex from Chaetoceros gracilis)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Unknown ligand (Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (17 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chaetoceros gracilis)
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
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 ]
- Dodecyl-alpha-d-maltoside (510 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)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (21 kDa, Protein from Chaetoceros gracilis)
- Unknown ligand (Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (29 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)
- Chlorophyll c1 (610 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a/b-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (23 kDa, Protein from Chaetoceros gracilis)
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- S1m1-type fcpii complex (240 kDa, Complex from Chaetoceros gracilis)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
Cryo-EM Structure of PSII at 2.22 angstrom resolution
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR
Commun Biol (2021) 4 pp. 382-382 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
Cryo-EM Structure of PSII at 2.20 angstrom resolution
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR
Commun Biol (2021) 4 pp. 382-382 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
Structure of the peripheral FCPI from diatom
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 6l4t
Q-score: 0.563
Nagao R, Kato K, Ifuku K, Suzuki T, Kumazawa M, Uchiyama I, Kashino Y, Dohmae N, Akimoto S, Shen JR, Miyazaki N, Akita F
Nat Commun (2020) [ DOI: doi:10.1038/s41467-020-16324-3 ]
- Fucoxanthin chlorophyll a/c-binding protein lhcr3 (22 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr12 (22 kDa, Protein from Chaetoceros gracilis)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr10 (32 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcq13 (24 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq3 (21 kDa, Protein from Chaetoceros gracilis)
- Peripheral fcpi (170 kDa, Complex from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr4 (29 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq5 (23 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq10 (26 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (30 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq11 (25 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)
Structure of the PSI-FCPI supercomplex from diatom
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 6l4u
Q-score: 0.587
Nagao R, Kato K, Ifuku K, Suzuki T, Kumazawa M, Uchiyama I, Kashino Y, Dohmae N, Akimoto S, Shen JR, Miyazaki N, Akita F
Nat Commun (2020) [ DOI: doi:10.1038/s41467-020-16324-3 ]
- Phylloquinone (450 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr3 (22 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a isomer (893 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcf6 (23 kDa, Protein from Chaetoceros gracilis)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Psi-fcpi (640 kDa, Complex from Chaetoceros gracilis)
- Photosystem i reaction center subunit psa28 (12 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 i reaction center subunit viii (3 kDa, Protein from Chaetoceros gracilis)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr9 (22 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr2 (21 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr11 (29 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr15 (24 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chaetoceros gracilis)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Chaetoceros gracilis)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (3s,3'r,5r,6s,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol (582 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr10 (32 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcq13 (24 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq3 (21 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Fucoxanthin chlorophyll a/c-binding protein lhcr4 (29 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq5 (23 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq10 (26 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr8 (21 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq8 (30 kDa, Protein from Chaetoceros gracilis)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Chaetoceros gracilis)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcq11 (25 kDa, Protein from Chaetoceros gracilis)
- Unknown protein 1 (11 kDa, Protein from Chaetoceros gracilis)
- Fucoxanthin chlorophyll a/c-binding protein lhcr12 (22 kDa, Protein from Chaetoceros gracilis)
- Iron/sulfur cluster (351 Da, Ligand)
Structure of PSI-isiA supercomplex from Thermosynechococcus vulcanus
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 6k33
Q-score: 0.445
Akita F, Nagao R, Kato K, Nakajima Y, Yokono M, Ueno Y, Suzuki T, Dohmae N, Shen JR, Akimoto S, Miyazaki N
Commun Biol (2020) 3 pp. 232-232 [ Pubmed: 32393811 DOI: doi:10.1038/s42003-020-0949-6 ]
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus vulcanus)
- Iron stress in-duced protein a (39 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Thermosynechococcus vulcanus)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit psax (3 kDa, Protein from Thermosynechococcus vulcanus)
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus vulcanus)
- Psi-isia (1 MDa, Complex from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus vulcanus)
- Iron/sulfur cluster (351 Da, Ligand)
Structure of PSI from H. hongdechloris grown under white light condition
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 6kmw
Q-score: 0.645
Kato K, Shinoda T, Nagao R, Akimoto S, Suzuki T, Dohmae N, Chen M, Allakhverdiev SI, Shen JR, Akita F, Miyazaki N, Tomo T
Nat Commun (2020) 11 pp. 238-238 [ DOI: doi:10.1038/s41467-019-13898-5 Pubmed: 31932639 ]
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Halomicronema hongdechloris C2206)
- White psi (Complex from Halomicronema hongdechloris C2206)
- Photosystem i p700 chlorophyll a apoprotein a1 (84 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Halomicronema hongdechloris C2206)
- Unknown ligand (Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Halomicronema hongdechloris C2206)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Halomicronema hongdechloris C2206)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Halomicronema hongdechloris C2206)
Structure of PSI from H. hongdechloris grown under far-red light condition
Resolution: 2.41 Å
EM Method: Single-particle
Fitted PDBs: 6kmx
Q-score: 0.649
Kato K, Shinoda T, Nagao R, Akimoto S, Suzuki T, Dohmae N, Chen M, Allakhverdiev SI, Shen JR, Akita F, Miyazaki N, Tomo T
Nat Commun (2020) 11 pp. 238-238 [ DOI: doi:10.1038/s41467-019-13898-5 Pubmed: 31932639 ]
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Halomicronema hongdechloris C2206)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Halomicronema hongdechloris C2206)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit psak (9 kDa, Protein from Halomicronema hongdechloris C2206)
- Chlorophyll f (905 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (87 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Halomicronema hongdechloris C2206)
- Far-red psi (Complex from Halomicronema hongdechloris)
- Water (18 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit viii (7 kDa, Protein from Halomicronema hongdechloris C2206)
- Unknown ligand (Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Halomicronema hongdechloris C2206)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosystem i reaction center subunit xi (20 kDa, Protein from Halomicronema hongdechloris C2206)