Cryo-EM Structure of primitive cyanobacterium 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 p700 chlorophyll a apoprotein a1 (86 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i reaction center subunit z (3 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit iii (19 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i reaction center subunit xii (3 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i iron-sulfur center (8 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Menaquinone-4 (444 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Psi trimer (1 MDa, Complex from Gloeobacter violaceus PCC 7421)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Water (18 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Unknown protein (2 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))
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / 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 ]
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (24 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chaetoceros gracilis)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (16 kDa, Protein from Chaetoceros gracilis)
- Unknown ligand (Ligand)
- Photosystem ii subunit (4 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein j (3 kDa, Protein from Chaetoceros gracilis)
- Extrinsic protein in photosystem ii (10 kDa, Protein from Chaetoceros gracilis)
- 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)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii d2 protein (37 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein h (7 kDa, Protein from Chaetoceros gracilis)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Extrinsic protein in photosystem ii (16 kDa, Protein from Chaetoceros gracilis)
- Bicarbonate ion (61 Da, Ligand)
- Unknown protein 1 (2 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii cp47 reaction center protein (53 kDa, Protein from Chaetoceros gracilis)
- Fe (ii) ion (55 Da, Ligand)
- Cytochrome b559 subunit alpha (8 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (19 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 ii reaction center x protein (3 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Chaetoceros gracilis)
- Water (18 Da, Ligand)
- Cytochrome b559 subunit beta (3 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)
- Photosystem ii protein d1 (37 kDa, Protein from Chaetoceros gracilis)
- Pheophytin a (871 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Extrinsic protein in photosystem ii (26 kDa, Protein from Chaetoceros gracilis)
- C2s2m2-type psii-fcpii supercomplex (1 MDa, Complex 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)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chaetoceros gracilis)
- Unknown protein 0 (2 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chaetoceros gracilis)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (19 kDa, Protein from Chaetoceros gracilis)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem ii reaction center protein w (5 kDa, Protein from Chaetoceros gracilis)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (17 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (18 kDa, Protein from Chaetoceros gracilis)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chaetoceros gracilis)
- Ca-mn4-o5 cluster (339 Da, Ligand)
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 ]
- Fcpb5, fucoxanthin chlorophyll a/c-binding protein (29 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 Da, Ligand)
- Fcpb4, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- S1m1-type fcpii complex (240 kDa, Complex from Chaetoceros gracilis)
- Chlorophyll a/b-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Fcpb6, fucoxanthin chlorophyll a/c-binding protein (23 kDa, Protein from Chaetoceros gracilis)
- Fcpb7, fucoxanthin chlorophyll a/c-binding protein (21 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)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Fcpb2, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- Unknown ligand (Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Fcpb3, fucoxanthin chlorophyll a/c-binding protein (22 kDa, Protein from Chaetoceros gracilis)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a (893 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)
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 ]
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanophora paradoxa)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanophora paradoxa)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit ii, cyanelle (23 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanophora paradoxa)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit psak 1 (15 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanophora paradoxa)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Cyanophora paradoxa)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Psi monomer1 (350 kDa, Complex from Cyanophora paradoxa)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanophora paradoxa)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanophora paradoxa)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit xii (3 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 ]
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanophora paradoxa)
- Phylloquinone (450 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanophora paradoxa)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanophora paradoxa)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanophora paradoxa)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit ii, cyanelle (23 kDa, Protein from Cyanophora paradoxa)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Cyanophora paradoxa)
- Psi monomer2 (350 kDa, Complex from Cyanophora paradoxa)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Cyanophora paradoxa)
- Iron/sulfur cluster (351 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanophora paradoxa)
- Beta-carotene (536 Da, Ligand)
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 ]
- Photosystem i reaction center subunit viii (3 kDa, Protein from Cyanophora paradoxa)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Cyanophora paradoxa)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i reaction center subunit ii, cyanelle (23 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Cyanophora paradoxa)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit psak 1 (15 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Cyanophora paradoxa)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Cyanophora paradoxa)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Psi tetramer (1 MDa, Complex from Cyanophora paradoxa)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Cyanophora paradoxa)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Cyanophora paradoxa)
- Photosystem i iron-sulfur center (8 kDa, Protein from Cyanophora paradoxa)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit xii (3 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 [ DOI: doi:10.1038/s42003-020-0949-6 Pubmed: 32393811 ]
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus vulcanus)
- Phylloquinone (450 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 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)
- Beta-carotene (536 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Water (18 Da, Ligand)
- Iron stress in-duced protein a (39 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus vulcanus)
- Calcium ion (40 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus vulcanus)
- Psi-isia (1 MDa, Complex from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit psax (3 kDa, Protein from Thermosynechococcus vulcanus)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)