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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 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 ]
- Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein w (5 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
- Cytochrome b559 subunit beta (3 kDa, Protein from Chaetoceros gracilis)
- C2s2m2-type psii-fcpii supercomplex (1 MDa, Complex from Chaetoceros gracilis)
- Photosystem ii reaction center protein z (6 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)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
- Fe (ii) ion (55 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii protein d1 (37 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (16 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii d2 protein (37 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chaetoceros gracilis)
- Cytochrome c-550 (14 kDa, Protein from Chaetoceros gracilis)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (17 kDa, Protein from Chaetoceros gracilis)
- Digalactosyl diacyl glycerol (dgdg) (949 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 reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii subunit (4 kDa, Protein from Chaetoceros gracilis)
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (24 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
- Beta-carotene (536 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Unknown ligand (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)
- Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (16 kDa, Protein from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Chlorophyll a/b-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 ]
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (22 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)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (21 kDa, Protein from Chaetoceros gracilis)
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (29 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (23 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (22 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)
- Water (18 Da, Ligand)
- 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)
- Chlorophyll a/b-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Unknown ligand (Ligand)
Structure of Wild-type PSI monomer1 from Cyanophora paradoxa
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7dr0
Q-score: 0.53
Kato K, Nagao R, Ueno Y, Yokono M, Suzuki T, Jiang TY, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR
bioRxiv (2022) [ DOI: doi:10.1101/2022.01.03.474851 ]
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Cyanophora paradoxa)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanophora paradoxa)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Psi monomer1 (350 kDa, Complex from Cyanophora paradoxa)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit psak 1 (15 kDa, Protein from Cyanophora paradoxa)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit ii, cyanelle (23 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanophora paradoxa)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Cyanophora paradoxa)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Cyanophora paradoxa)
Structure of Wild-type PSI monomer2 from Cyanophora paradoxa
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7dr1
Q-score: 0.525
Kato K, Nagao R, Ueno Y, Yokono M, Suzuki T, Jiang TY, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR
bioRxiv (2022) [ DOI: doi:10.1101/2022.01.03.474851 ]
- Psi monomer2 (350 kDa, Complex from Cyanophora paradoxa)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanophora paradoxa)
- Chlorophyll a (893 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit ii, cyanelle (23 kDa, Protein from Cyanophora paradoxa)
- Beta-carotene (536 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanophora paradoxa)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Cyanophora paradoxa)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanophora paradoxa)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanophora paradoxa)
Structure of Wild-type PSI tetramer from Cyanophora paradoxa
Kato K, Nagao R, Ueno Y, Yokono M, Suzuki T, Jiang TY, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR
bioRxiv (2022) [ DOI: doi:10.1101/2022.01.03.474851 ]
- Psi tetramer (1 MDa, Complex from Cyanophora paradoxa)
Structure of GraFix PSI tetramer from Cyanophora paradoxa
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7dr2
Q-score: 0.374
Kato K, Nagao R, Ueno Y, Yokono M, Suzuki T, Jiang TY, Dohmae N, Akita F, Akimoto S, Miyazaki N, Shen JR
bioRxiv (2022) [ DOI: doi:10.1101/2022.01.03.474851 ]
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Cyanophora paradoxa)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanophora paradoxa)
- Psi tetramer (1 MDa, Complex from Cyanophora paradoxa)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit psak 1 (15 kDa, Protein from Cyanophora paradoxa)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit ii, cyanelle (23 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanophora paradoxa)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Cyanophora paradoxa)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Cyanophora paradoxa)
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 psax (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a (893 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Psi-isia (1 MDa, Complex from Thermosynechococcus vulcanus)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a isomer (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus vulcanus)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Iron stress in-duced protein a (39 kDa, Protein from Thermosynechococcus vulcanus)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus vulcanus)
- 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 ]
- Chlorophyll a (893 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- 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))
- 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 reaction center subunit ix (5 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Chlorophyll a isomer (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit xii (4 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i 4.8 kda protein (4 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Beta-carotene (536 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 iv (7 kDa, Protein from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit viii (5 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))
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)