PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)
Resolution: 1.92 Å
EM Method: Single-particle
Fitted PDBs: 8wey
Q-score: 0.662
Kato K, Hamaguchi T, Kumazawa M, Nakajima Y, Ifuku K, Hirooka S, Hirose Y, Miyagishima SY, Suzuki T, Kawakami K, Dohmae N, Yonekura K, Shen JR, Nagao R
PNAS (2024) 121 pp. e2319658121-e2319658121 [ Pubmed: 38442179 DOI: doi:10.1073/pnas.2319658121 ]
- Photosystem i reaction center subunit x (7 kDa, Protein from Cyanidium caldarium)
- Phylloquinone (450 Da, Ligand)
- Lhcr3 (23 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Cyanidium caldarium)
- Lhcr2 (24 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit iv (6 kDa, Protein from Cyanidium caldarium)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanidium caldarium)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanidium caldarium)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- (1~{r})-3,5,5-trimethyl-4-[(1~{e},3~{e},5~{e},7~{e},9~{e},11~{e},13~{e},15~{e},17~{e})-3,7,12,16-tetramethyl-18-[(4~{r} )-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol (568 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanidium caldarium)
- Photosystem i subunit o (16 kDa, Protein from Cyanidium caldarium)
- Water (18 Da, Ligand)
- Psi-lhci (550 kDa, Complex from Cyanidium caldarium)
- Lhcr1 (24 kDa, Protein from Cyanidium caldarium)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Unknown ligand (Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanidium caldarium)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Cyanidium caldarium)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Structure of the Anabaena PSI-monomer-IsiA supercomplex
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 7y3f
Q-score: 0.526
Nagao R, Kato K, Hamaguchi T, Ueno Y, Tsuboshita N, Shimizu S, Furutani M, Ehira S, Nakajima Y, Kawakami K, Suzuki T, Dohmae N, Akimoto S, Yonekura K, Shen JR
Nat Commun (2023) 14 pp. 920-920 [ Pubmed: 36805598 DOI: doi:10.1038/s41467-023-36504-1 ]
- Photosystem i reaction center subunit ix (5 kDa, Protein from Nostoc sp.)
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Nostoc sp.)
- Phylloquinone (450 Da, Ligand)
- Psam (4 kDa, Protein from Nostoc sp.)
- Photosystem i iron-sulfur center (8 kDa, Protein from Nostoc sp.)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Nostoc sp.)
- Chlorophyll a (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Isia (27 kDa, Protein from Nostoc sp.)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit viii (5 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit xi (51 kDa, Protein from Nostoc sp.)
- Unknown (6 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Nostoc sp.)
- Water (18 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 1 (83 kDa, Protein from Nostoc sp.)
- Psi-monomer-isia (640 kDa, Complex from Nostoc sp.)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i 4.8 kda protein (4 kDa, Protein from Nostoc sp.)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM structure of a primordial cyanobacterial photosystem I
Resolution: 2.04 Å
EM Method: Single-particle
Fitted PDBs: 7f4v
Q-score: 0.752
Kato K, Hamaguchi T, Nagao R, Kawakami K, Ueno Y, Suzuki T, Uchida H, Murakami A, Nakajima Y, Yokono M, Akimoto S, Dohmae N, Yonekura K, Shen JR
bioRxiv (2022) [ DOI: doi:10.1101/2021.09.29.462462 ]
- Photosystem i reaction center subunit iv (7 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i reaction center subunit iii (19 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Menaquinone-4 (444 Da, Ligand)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Psi trimer (1 MDa, Complex from Gloeobacter violaceus PCC 7421)
- Photosystem i reaction center subunit z (3 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i p700 chlorophyll a apoprotein a2 (96 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Water (18 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (86 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Unknown protein (2 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i reaction center subunit ii (15 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Structure of monomeric photosystem II
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 7eda
Q-score: 0.622
Yu H, Hamaguchi T, Nakajima Y, Kato K, Kawakami K, Akita F, Yonekura K, Shen JR
Biochim Biophys Acta Bioenerg (2021) 1862 pp. 148471-148471 [ Pubmed: 34216574 DOI: doi:10.1016/j.bbabio.2021.148471 ]
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii cp47 reaction center protein (55 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein h (6 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
- 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)
- Photosystem ii 12 kda extrinsic protein (11 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein j (4 kDa, Protein from Thermosynechococcus vulcanus)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
- Unknown ligand (949 Da, Ligand)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Heme c (618 Da, Ligand)
- Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome b559 subunit beta (5 kDa, Protein from Thermosynechococcus vulcanus)
- Water (18 Da, Ligand)
- Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome c-550 (18 kDa, Protein from Thermosynechococcus vulcanus)
- Bicarbonate ion (61 Da, Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Photosystem ii (Complex from Thermosynechococcus vulcanus)
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 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
- 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)
- Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein h (7 kDa, Protein from Thermosynechococcus vulcanus)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein j (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Cytochrome b559 subunit beta (3 kDa, Protein from Thermosynechococcus vulcanus)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Heme c (618 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Unknown ligand (Ligand)
- Chloride ion (35 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome c-550 (15 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii 12 kda extrinsic protein (10 kDa, Protein from Thermosynechococcus vulcanus)
- Bicarbonate ion (61 Da, Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome b559 subunit alpha (9 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 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
- 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)
- Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein h (7 kDa, Protein from Thermosynechococcus vulcanus)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein j (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Cytochrome b559 subunit beta (3 kDa, Protein from Thermosynechococcus vulcanus)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Heme c (618 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Unknown ligand (Ligand)
- Chloride ion (35 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome c-550 (15 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii 12 kda extrinsic protein (10 kDa, Protein from Thermosynechococcus vulcanus)
- Bicarbonate ion (61 Da, Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome b559 subunit alpha (9 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 [ 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)
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: