Organization and energy transfer in a huge diatom PSI-FCPI supercomplex
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 6ly5
Q-score: 0.517
Xu C, Pi X, Huang Y, Han G, Chen X, Qin X, Huang G, Zhao S, Yang Y, Kuang T, Wang W, Sui SF, Shen JR
Nat Commun (2020) 11 pp. 5081-5081 [ DOI: doi:10.1038/s41467-020-18867-x Pubmed: 33033236 ]
- Fcpi (21 kDa, Protein from Chaetoceros gracilis)
- Fcpi-16 (32 kDa, Protein from Chaetoceros gracilis)
- Psas (11 kDa, Protein from Chaetoceros gracilis)
- Psac (8 kDa, Protein from Chaetoceros gracilis)
- Psal (19 kDa, Protein from Chaetoceros gracilis)
- Phylloquinone (450 Da, Ligand)
- Fcpi-19 (19 kDa, Protein from Chaetoceros gracilis)
- Psad (14 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll a (893 Da, Ligand)
- Psaa (82 kDa, Protein from Chaetoceros gracilis)
- Fcpi-8 (23 kDa, Protein from Chaetoceros gracilis)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Fcpi-5 (23 kDa, Protein from Chaetoceros gracilis)
- Psae (7 kDa, Protein from Chaetoceros gracilis)
- Beta-carotene (536 Da, Ligand)
- Fcpi-2 (17 kDa, Protein from Chaetoceros gracilis)
- Fcpi-13 (22 kDa, Protein from Chaetoceros gracilis)
- Fcpi-14 (24 kDa, Protein from Chaetoceros gracilis)
- Fcpi-7 (18 kDa, Protein from Chaetoceros gracilis)
- Fcpi-21 (24 kDa, Protein from Chaetoceros gracilis)
- Fcpi-1 (24 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)
- Psaj (4 kDa, Protein from Chaetoceros gracilis)
- Chlorophyll c1 (610 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)
- Fcpi-17 (21 kDa, Protein from Chaetoceros gracilis)
- Fcpi-24 (26 kDa, Protein from Chaetoceros gracilis)
- Fcpi-12 (22 kDa, Protein from Chaetoceros gracilis)
- Psaf (17 kDa, Protein from Chaetoceros gracilis)
- Fcpi-3 (21 kDa, Protein from Chaetoceros gracilis)
- Fcpi-4 (26 kDa, Protein from Chaetoceros gracilis)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Psam (3 kDa, Protein from Chaetoceros gracilis)
- Psab (82 kDa, Protein from Chaetoceros gracilis)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Psai (4 kDa, Protein from Chaetoceros gracilis)
- Psar (14 kDa, Protein from Chaetoceros gracilis)
- Fcpi-6 (22 kDa, Protein from Chaetoceros gracilis)
- A huge diatom psi-fcpi supercomplex (Complex from Chaetoceros gracilis)
- Fcpi-9 (21 kDa, Protein from Chaetoceros gracilis)
- Fcpi-10 (21 kDa, Protein from Chaetoceros gracilis)
- Fcpi-11 (21 kDa, Protein from Chaetoceros gracilis)
- Fcpi-23 (27 kDa, Protein from Chaetoceros gracilis)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
Dunaliella Photosystem I Supercomplex
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 6sl5
Q-score: 0.53
Caspy I, Malavath T, Klaiman D, Fadeeva M, Shkolnisky Y, Nelson N
Biochim Biophys Acta Bioenerg (2020) 1861 pp. 148253-148253 [ Pubmed: 32569661 DOI: doi:10.1016/j.bbabio.2020.148253 ]
- Psah (10 kDa, Protein from Dunaliella salina)
- Phylloquinone (450 Da, Ligand)
- Trimethyl-[(2~{r})-1-oxidanyl-1-oxidanylidene-4-[(2~{s})-2-[(1~{s})-1-oxidanyloctadecoxy]-3-[(1~{r})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium (773 Da, Ligand)
- Lhca4 (23 kDa, Protein from Dunaliella salina)
- Chlorophyll a isomer (893 Da, Ligand)
- [(2~{r})-1-nonanoyloxy-3-[oxidanyl-[(2~{r},3~{s},5~{r},6~{r})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{z},8~{z})-heptadeca-5,8-dienoate (722 Da, Ligand)
- Psaf (18 kDa, Protein from Dunaliella salina)
- Chlorophyll a (893 Da, Ligand)
- Large dunaliella salina photosystem i-lhc supercomplex (Complex from Dunaliella salina)
- Lhca5 (21 kDa, Protein from Dunaliella salina)
- Chlorophyll b (907 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- Psae (7 kDa, Protein from Dunaliella salina)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Psal (16 kDa, Protein from Dunaliella salina)
- Calcium ion (40 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- Psak (8 kDa, Protein from Dunaliella salina)
- Psad (16 kDa, Protein from Dunaliella salina)
- Psai (4 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (21 kDa, Protein from Dunaliella salina)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Dunaliella salina)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Lhca2 (22 kDa, Protein from Dunaliella salina)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Dunaliella salina)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Dunaliella salina)
- Phosphatidylethanolamine (734 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Dunaliella salina)
- Photosystem i p700 chlorophyll a apoprotein a1 (81 kDa, Protein from Dunaliella salina)
- Lhca6 (19 kDa, Protein from Dunaliella salina)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Psao (9 kDa, Protein from Dunaliella salina)
- Octadecanal (268 Da, Ligand)
- Psag (10 kDa, Protein from Dunaliella salina)
Structure of cyanobacterial photosystem I-IsiA-flavodoxin supercomplex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6kif
Q-score: 0.36
Cao P, Cao D, Si L, Su X, Tian L, Chang W, Liu Z, Zhang X, Li M
Nat Plants (2020) 6 pp. 167-176 [ Pubmed: 32042157 DOI: doi:10.1038/s41477-020-0593-7 ]
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Phylloquinone (450 Da, Ligand)
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Chlorophyll a (893 Da, Ligand)
- Photosystem i-isia-flavodoxin supercomplex (Complex from Synechococcus elongatus PCC 7942)
- Photosystem i iron-sulfur center (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i psai protein (4 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit ii (15 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Flavodoxin (18 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Beta-carotene (536 Da, Ligand)
- Psam (3 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Flavin mononucleotide (456 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i reaction center subunit iv (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit xi (17 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Synechococcus elongatus (strain PCC 7942))
- Iron/sulfur cluster (351 Da, Ligand)
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 6igz
Q-score: 0.475
Qin X, Pi X, Wang W, Han G, Zhu L, Liu M, Cheng L, Shen JR, Kuang T, Sui SF
Nat Plants (2019) 5 pp. 263-272 [ Pubmed: 30850820 DOI: doi:10.1038/s41477-019-0379-y ]
- Psab (82 kDa, Protein from Bryopsis corticulans)
- Lhca-b (26 kDa, Protein from Bryopsis corticulans)
- Lhca-g (29 kDa, Protein from Bryopsis corticulans)
- Psad (21 kDa, Protein from Bryopsis corticulans)
- Psaf (25 kDa, Protein from Bryopsis corticulans)
- Phylloquinone (450 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Lhca-h (28 kDa, Protein from Bryopsis corticulans)
- Psi-lhci (Complex from Bryopsis corticulans)
- Psae (10 kDa, Protein from Bryopsis corticulans)
- Lhca-j (26 kDa, Protein from Bryopsis corticulans)
- Psah (14 kDa, Protein from Bryopsis corticulans)
- (6'r,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene (536 Da, Ligand)
- Heptyl 1-thiohexopyranoside (294 Da, Ligand)
- Psag (18 kDa, Protein from Bryopsis corticulans)
- Psak (12 kDa, Protein from Bryopsis corticulans)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Psai (3 kDa, Protein from Bryopsis corticulans)
- Lhca-d (30 kDa, Protein from Bryopsis corticulans)
- Lhca-i (24 kDa, Protein from Bryopsis corticulans)
- Psal (21 kDa, Protein from Bryopsis corticulans)
- Psaj (4 kDa, Protein from Bryopsis corticulans)
- Lhca-a (24 kDa, Protein from Bryopsis corticulans)
- Lhca-c (27 kDa, Protein from Bryopsis corticulans)
- Chlorophyll a (893 Da, Ligand)
- Psaa (83 kDa, Protein from Bryopsis corticulans)
- Psac (8 kDa, Protein from Bryopsis corticulans)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Bryopsis corticulans)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Photosystem I of Chlamydomonas reinhardtii
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 6ijj
Q-score: 0.537
Su X, Ma J, Pan X, Zhao X, Chang W, Liu Z, Zhang X, Li M
Nat Plants (2019) 5 pp. 273-281 [ Pubmed: 30850819 DOI: doi:10.1038/s41477-019-0380-5 ]
- Lhca3 (32 kDa, Protein from Chlamydomonas reinhardtii)
- Phylloquinone (450 Da, Ligand)
- Lhca8 (29 kDa, Protein from Chlamydomonas reinhardtii)
- Psai (10 kDa, Protein from Chlamydomonas reinhardtii)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlamydomonas reinhardtii psi with eight light harvesting antennae (Complex from Chlamydomonas reinhardtii)
- Chlorophyll a (893 Da, Ligand)
- Psaf (24 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Lhca1 (26 kDa, Protein from Chlamydomonas reinhardtii)
- Beta-carotene (536 Da, Ligand)
- Psae (16 kDa, Protein from Chlamydomonas reinhardtii)
- Psak (16 kDa, Protein from Chlamydomonas reinhardtii)
- Psab (82 kDa, Protein from Chlamydomonas reinhardtii)
- Lhca4 (31 kDa, Protein from Chlamydomonas reinhardtii)
- Lhca7 (26 kDa, Protein from Chlamydomonas reinhardtii)
- Psaa (83 kDa, Protein from Chlamydomonas reinhardtii)
- Lhca6 (35 kDa, Protein from Chlamydomonas reinhardtii)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Psaj (4 kDa, Protein from Chlamydomonas reinhardtii)
- Psac (8 kDa, Protein from Chlamydomonas reinhardtii)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Psad (21 kDa, Protein from Chlamydomonas reinhardtii)
- Psal (27 kDa, Protein from Chlamydomonas reinhardtii)
- Lhca5 (30 kDa, Protein from Chlamydomonas reinhardtii)
- Iron/sulfur cluster (351 Da, Ligand)
Cryo-EM structure of the red algal PSI-LHCR
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 5zgb
Q-score: 0.399
Pi X, Tian L, Dai HE, Qin X, Cheng L, Kuang T, Sui SF, Shen JR
PNAS (2018) 115 pp. 4423-4428 [ DOI: doi:10.1073/pnas.1722482115 Pubmed: 29632169 ]
- Psaa (82 kDa, Protein from Red alga)
- Lhcr3 (20 kDa, Protein from Red alga)
- Phylloquinone (450 Da, Ligand)
- (1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
- Psi-5lhcr (Complex from Cyanidioschyzon merolae)
- Lhcr1 (19 kDa, Protein from Red alga)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Psaf (21 kDa, Protein from Red alga)
- Psao (16 kDa, Protein from Red alga)
- Psad (15 kDa, Protein from Red alga)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Psam (3 kDa, Protein from Red alga)
- Psaj (4 kDa, Protein from Red alga)
- Psai (3 kDa, Protein from Red alga)
- Psab (82 kDa, Protein from Red alga)
- Psae (10 kDa, Protein from Red alga)
- Psac (8 kDa, Protein from Red alga)
- Psal (15 kDa, Protein from Red alga)
- (2s)-2,3-dihydroxypropyl octadecanoate (358 Da, Ligand)
- 1-dodecanol (186 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Beta-d-glucose (180 Da, Ligand)
- Lhcr2 (21 kDa, Protein from Red alga)
- Psak (6 kDa, Protein from Red alga)
- Iron/sulfur cluster (351 Da, Ligand)