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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 xi (15 kDa, Protein from Cyanidium caldarium)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanidium caldarium)
- Chlorophyll a (893 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)
- Lhcr3 (23 kDa, Protein from Cyanidium caldarium)
- Lhcr2 (24 kDa, Protein from Cyanidium caldarium)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanidium caldarium)
- Chlorophyll a isomer (893 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Cyanidium caldarium)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanidium caldarium)
- Lhcr1 (24 kDa, Protein from Cyanidium caldarium)
- Psi-lhci (550 kDa, Complex from Cyanidium caldarium)
- Photosystem i reaction center subunit iv (6 kDa, Protein from Cyanidium caldarium)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i subunit o (16 kDa, Protein from Cyanidium caldarium)
- Unknown ligand (Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanidium caldarium)
- Photosystem i reaction center subunit x (7 kDa, Protein from Cyanidium caldarium)
- Water (18 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanidium caldarium)
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 ]
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Nostoc sp.)
- Psam (4 kDa, Protein from Nostoc sp.)
- Photosystem i p700 chlorophyll a apoprotein a2 1 (83 kDa, Protein from Nostoc sp.)
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Nostoc sp.)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit ix (5 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit viii (5 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Nostoc sp.)
- Photosystem i 4.8 kda protein (4 kDa, Protein from Nostoc sp.)
- Chlorophyll a isomer (893 Da, Ligand)
- Psi-monomer-isia (640 kDa, Complex from Nostoc sp.)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Nostoc sp.)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i iron-sulfur center (8 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.)
- Phylloquinone (450 Da, Ligand)
- Isia (27 kDa, Protein from Nostoc sp.)
- Water (18 Da, Ligand)
- Unknown (6 kDa, Protein from Nostoc sp.)
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 xii (3 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Unknown protein (2 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i reaction center subunit xi (15 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i reaction center subunit iv (7 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))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit z (3 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))
- Iron/sulfur cluster (351 Da, Ligand)
- Menaquinone-4 (444 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (86 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Beta-carotene (536 Da, Ligand)
- Water (18 Da, Ligand)
- Psi trimer (1 MDa, Complex from Gloeobacter violaceus PCC 7421)
Structure of the far-red light utilizing photosystem I of Acaryochloris marina
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7coy
Q-score: 0.553
Hamaguchi T, Kawakami K, Shinzawa-Itoh K, Inoue-Kashino N, Itoh S, Ifuku K, Yamashita E, Maeda K, Yonekura K, Kashino Y
Nat Commun (2021) 12 pp. 2333-2333 [ DOI: doi:10.1038/s41467-021-22502-8 Pubmed: 33879791 ]
- Photosystem i complex from acaryochloris marina (Complex from Acaryochloris marina)
- Photosystem i iron-sulfur center (8 kDa, Protein from Acaryochloris marina MBIC110017)
- Photosystem i reaction center subunit iv (9 kDa, Protein from Acaryochloris marina MBIC110017)
- Photosystem i protein psaf (17 kDa, Protein from Acaryochloris marina MBIC110017)
- Photosystem i reaction center subunit ix (5 kDa, Protein from Acaryochloris marina MBIC110017)
- Photosystem i protein psal (15 kDa, Protein from Acaryochloris marina MBIC 11017)
- Photosystem i protein psa27 (3 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem i protein psad (15 kDa, Protein from Acaryochloris marina MBIC110017)
- Photosystem i protein psam (3 kDa, Protein from Acaryochloris marina MBIC11017)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Acaryochloris marina MBIC110017)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Acaryochloris marina MBIC11017)
- Photosystem i reaction center subunit psak (9 kDa, Protein from Acaryochloris marina MBIC 11017)
- Chlorophyll d (895 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll d isomer (895 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Unknown ligand (Ligand)
- Phylloquinone (450 Da, Ligand)
- Water (18 Da, Ligand)