Structure of high-light grown Chlorella ohadii photosystem I
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 6zzy
Q-score: 0.561
Caspy I, Neumann E, Fadeeva M, Liveanu V, Savitsky A, Frank A, Kalisman YL, Shkolnisky Y, Murik O, Treves H, Hartmann V, Nowaczyk MM, Schuhmann W, Rogner M, Willner I, Kaplan A, Schuster G, Nelson N, Lubitz W, Nechushtai R
Nat Plants (2021) 7 pp. 1314-1322 [ Pubmed: 34462576 DOI: doi:10.1038/s41477-021-00983-1 ]
- Psi-f (18 kDa, Protein from Freshwater green alga)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- Psi subunit v (16 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Freshwater green alga)
- Phylloquinone (450 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Freshwater green alga)
- High light grown chlorella ohadii photosystem i (1 MDa, Complex from Chlorella ohadii)
- [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium (440 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Freshwater green alga)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Freshwater green alga)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Freshwater green alga)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (787 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Freshwater green alga)
- Photosystem i reaction center subunit vi-chloroplastic-like (10 kDa, Protein from Freshwater green alga)
- 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)
- Psi-k (8 kDa, Protein from Freshwater green alga)
- Beta-carotene (536 Da, Ligand)
- Glutathione reductase (26 kDa, Protein from Freshwater green alga)
- 2-(2-azanylethanoylamino)ethanoic acid (132 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- (2z,4e)-5-[(1s)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid (264 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Freshwater green alga)
- Sphingosine (299 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- (1~{s})-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~{s})-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 iron-sulfur center (8 kDa, Protein from Freshwater green alga)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Freshwater green alga)
- Oleic acid (282 Da, Ligand)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Freshwater green alga)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (10 kDa, Protein from Freshwater green alga)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (15 kDa, Protein from Freshwater green alga)
- (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)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Freshwater green alga)
- (3~{e},5~{e},7~{e})-6-methyl-8-[(6~{r})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one (260 Da, Ligand)
- Ergosterol (396 Da, Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Structure of small high-light grown Chlorella ohadii photosystem I
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7a4p
Q-score: 0.278
Caspy I, Neumann E, Fadeeva M, Liveanu V, Savitsky A, Frank A, Kalisman YL, Shkolnisky Y, Murik O, Treves H, Hartmann V, Nowaczyk MM, Schuhmann W, Rogner M, Willner I, Kaplan A, Schuster G, Nelson N, Lubitz W, Nechushtai R
Nat Plants (2021) 7 pp. 1314-1322 [ Pubmed: 34462576 DOI: doi:10.1038/s41477-021-00983-1 ]
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Chlorella ohadii)
- Beta,beta-caroten-4-one (550 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Small high light grown chlorella ohadii photosystem i (900 kDa, Complex from Chlorella ohadii)
- Photosystem i reaction center subunit vi-chloroplastic-like (329 Da, Protein from Chlorella ohadii)
- [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate-oxy)-ethyl]-trimethylammonium (440 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (15 kDa, Protein from Chlorella ohadii)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Chlorella ohadii)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit chloroplastic (10 kDa, Protein from Chlorella ohadii)
- Chlorophyll b (907 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphocholine (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)
- Psi-f (18 kDa, Protein from Chlorella ohadii)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Chlorella ohadii)
- Psi-k (8 kDa, Protein from Chlorella ohadii)
- Beta-carotene (536 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Chlorella ohadii)
- Glutathione reductase (26 kDa, Protein from Chlorella ohadii)
- 2-(2-azanylethanoylamino)ethanoic acid (132 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Sphingosine (299 Da, Ligand)
- Tripalmitoylglycerol (807 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Chlorella ohadii)
- (2s)-3-{[(r)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate (453 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Chlorella ohadii)
- (1~{s})-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~{s})-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)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Chlorella ohadii)
- Oleic acid (282 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Chlorella ohadii)
- Chlorophyll a-b binding protein, chloroplastic (25 kDa, Protein from Chlorella ohadii)
- Psi subunit v (16 kDa, Protein from Chlorella ohadii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Phosphatidylethanolamine (734 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)
- Photosystem i p700 chlorophyll a apoprotein a2 (81 kDa, Protein from Chlorella ohadii)
- (3~{e},5~{e},7~{e})-6-methyl-8-[(6~{r})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one (260 Da, Ligand)
- Ergosterol (396 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Chlorella ohadii)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (24 kDa, Protein from Chlorella ohadii)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Plant PSI-ferredoxin supercomplex
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6yac
Q-score: 0.601
Caspy I, Borovikova-Sheinker A, Klaiman D, Shkolnisky Y, Nelson N
Nat Plants (2020) 6 pp. 1300-1305 [ DOI: doi:10.1038/s41477-020-00779-9 Pubmed: 33020607 ]
- Psaf (17 kDa, Protein from Pea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Pea)
- Chlorophyll a-b binding protein p4, chloroplastic (21 kDa, Protein from Pea)
- Phylloquinone (450 Da, Ligand)
- Ferredoxin-1, chloroplastic (10 kDa, Protein from Pea)
- Psad (16 kDa, Protein from Pea)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- 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)
- Beta-carotene (536 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Pea)
- Psal (16 kDa, Protein from Pea)
- Calcium ion (40 Da, Ligand)
- Psae (7 kDa, Protein from Pea)
- (1~{s})-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~{s})-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)
- Psag (10 kDa, Protein from Pea)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Pea)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Pea)
- Psah (9 kDa, Protein from Pea)
- Chlorophyll a-b binding protein 3, chloroplastic (24 kDa, Protein from Pea)
- Water (18 Da, Ligand)
- Lhca1 (21 kDa, Protein from Pea)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit x psak (8 kDa, Protein from Pea)
- Pea photosystem i in complex with ferredoxin (660 kDa, Complex from Pisum sativum)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Pea)
- (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)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Pea)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
Plant PSI-ferredoxin-plastocyanin supercomplex
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6yez
Q-score: 0.536
Caspy I, Borovikova-Sheinker A, Klaiman D, Shkolnisky Y, Nelson N
Nat Plants (2020) 6 pp. 1300-1305 [ DOI: doi:10.1038/s41477-020-00779-9 Pubmed: 33020607 ]
- Psaf (17 kDa, Protein from Pea)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Garden pea)
- Psad (16 kDa, Protein from Pea)
- Lhca1 (21 kDa, Protein from Pea)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Psae (7 kDa, Protein from Pea)
- Chlorophyll b (907 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a-b binding protein p4, chloroplastic (21 kDa, Protein from Garden pea)
- Triple complex of photosystem i bound to ferredoxin and plastocyanin (660 kDa, Complex from Pisum sativum)
- Beta-carotene (536 Da, Ligand)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Psal (16 kDa, Protein from Pea)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Garden pea)
- Calcium ion (40 Da, Ligand)
- Plastocyanin, chloroplastic (10 kDa, Protein from Garden pea)
- Photosystem i reaction center subunit x psak (8 kDa, Protein from Garden pea)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Garden pea)
- (1~{s})-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~{s})-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)
- Psag (10 kDa, Protein from Pea)
- Water (18 Da, Ligand)
- Chlorophyll a-b binding protein 3, chloroplastic (24 kDa, Protein from Garden pea)
- Psah (10 kDa, Protein from Pea)
- Iron/sulfur cluster (351 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (22 kDa, Protein from Garden pea)
- (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)
- Photosystem i iron-sulfur center (8 kDa, Protein from Garden pea)
- Copper (ii) ion (63 Da, Ligand)
- Psaj (4 kDa, Protein from Pea)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Ferredoxin-1, chloroplastic (10 kDa, Protein from Garden pea)