Cryo-EM Structure of PSII at 1.95 angstrom resolution
Resolution: 1.95 Å
EM Method: Single-particle
Fitted PDBs: 7d1t
Q-score: 0.776
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR
Commun Biol (2021) 4 pp. 382-382 [ DOI: doi:10.1038/s42003-021-01919-3 Pubmed: 33753866 ]
- Cytochrome c-550 (15 kDa, Protein from Thermosynechococcus vulcanus)
- Heme c (618 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein h (7 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii 12 kda extrinsic protein (10 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Thermosynechococcus vulcanus)
- Unknown ligand (Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
- Bicarbonate ion (61 Da, Ligand)
- Water (18 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Thermosynechococcus vulcanus)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Cytochrome b559 subunit beta (3 kDa, Protein from Thermosynechococcus vulcanus)
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein j (3 kDa, Protein from Thermosynechococcus vulcanus)
- Chloride ion (35 Da, Ligand)
- Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
- 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)
- Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
Cryo-EM Structure of PSII at 2.08 angstrom resolution
Resolution: 2.08 Å
EM Method: Single-particle
Fitted PDBs: 7d1u
Q-score: 0.757
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR
Commun Biol (2021) 4 pp. 382-382 [ DOI: doi:10.1038/s42003-021-01919-3 Pubmed: 33753866 ]
- Cytochrome c-550 (15 kDa, Protein from Thermosynechococcus vulcanus)
- Heme c (618 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein h (7 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii 12 kda extrinsic protein (10 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Thermosynechococcus vulcanus)
- Unknown ligand (Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
- Bicarbonate ion (61 Da, Ligand)
- Water (18 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Thermosynechococcus vulcanus)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Cytochrome b559 subunit beta (3 kDa, Protein from Thermosynechococcus vulcanus)
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein j (3 kDa, Protein from Thermosynechococcus vulcanus)
- Chloride ion (35 Da, Ligand)
- Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
- 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)
- Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
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 [ DOI: doi:10.1038/s42003-021-01919-3 Pubmed: 33753866 ]
- 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 [ DOI: doi:10.1038/s42003-021-01919-3 Pubmed: 33753866 ]
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
Cryo-EM Structure of PSII at 1.95 angstrom resolution
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen J
bioRxiv (2020) [ DOI: 10.1101/2020.10.18.344648 ]
Image sets:
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 reaction center subunit psak (8 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus vulcanus)
- Water (18 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit psax (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus vulcanus)
- Iron stress in-duced protein a (39 kDa, Protein from Thermosynechococcus vulcanus)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Thermosynechococcus vulcanus)
- Calcium ion (40 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Psi-isia (1 MDa, Complex from Thermosynechococcus vulcanus)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus vulcanus)
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 ]
- Photosystem i reaction center subunit viii (4 kDa, Protein from Halomicronema hongdechloris C2206)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Halomicronema hongdechloris C2206)
- Water (18 Da, Ligand)
- Unknown ligand (Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i p700 chlorophyll a apoprotein a1 (84 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i iron-sulfur center (8 kDa, Protein from Halomicronema hongdechloris C2206)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- White psi (Complex from Halomicronema hongdechloris C2206)
- Iron/sulfur cluster (351 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
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 ]
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Chlorophyll f (905 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Halomicronema hongdechloris C2206)
- Far-red psi (Complex from Halomicronema hongdechloris)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Halomicronema hongdechloris C2206)
- Water (18 Da, Ligand)
- Unknown ligand (Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Halomicronema hongdechloris C2206)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit psak (9 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i p700 chlorophyll a apoprotein a1 (87 kDa, Protein from Halomicronema hongdechloris C2206)
- Iron/sulfur cluster (351 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit xi (20 kDa, Protein from Halomicronema hongdechloris C2206)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit viii (7 kDa, Protein from Halomicronema hongdechloris C2206)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Halomicronema hongdechloris C2206)
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 [ DOI: doi:10.1038/s41467-019-12942-8 Pubmed: 31666526 ]
- Photosystem i reaction center subunit psak 1 (8 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))
- Photosystem i 4.8 kda protein (4 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))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Photosystem i reaction center subunit xii (4 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Photosystem i reaction center subunit ix (5 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Photosystem i iron-sulfur center (8 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Psi tetramer (1 MDa, Complex from Nostoc sp. PCC 7120)
- Photosystem i reaction center subunit xi (18 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Phylloquinone (450 Da, Ligand)
- 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 viii (5 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Iron/sulfur cluster (351 Da, Ligand)
- 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))
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
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 [ DOI: doi:10.1038/s41467-019-12942-8 Pubmed: 31666526 ]
- Psi dimer (700 kDa, Complex from Nostoc sp. PCC 7120)